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OpenEye CUP XXIII talk: ML/MM REPEX/ATM FEP/MBAR RBFEs and You - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2023/7/16/cadd-grc-2023-talk monthly 0.5 2024-03-09 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/0e85b1ef-b592-47d0-8dfd-8fbf9d36341c/2023+CADD+GRC+first+slide.jpg News - CADD GRC 2023 talk - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/10/24/celebrating-ten-years-at-mskcc monthly 0.5 2022-10-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/661499be-3dcb-452f-bead-113238fcbf9c/ski-talk.jpg News - Celebrating ten years at MSKCC - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/b7bbbda5-9ea1-4c93-8ed1-d3cc6242b85b/mskcc-thanks.jpg News - Celebrating ten years at MSKCC - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/7/15/mmsml-talk monthly 0.5 2022-07-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/4c12c494-48ff-4602-a318-d64734b82351/PRBB.jpg News - Barcelona MMSML talk: Teaching free energy calculations to learn - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/5/30/recomb-2022-talk-the-covid-moonshot-and-the-new-asap-avidd-center monthly 0.5 2022-05-31 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1d865c1d-952f-4bf2-8bf3-9e05d2b980bc/recomb2022.jpg News - RECOMB 2022 talk: The COVID Moonshot and the new ASAP AViDD Center - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/6/27/nih-awards-initial-68m-for-ai-driven-structure-enabled-antiviral-platform-asap-for-open-science-discovery-of-oral-antivirals-for-pandemic-preparedness monthly 0.5 2022-06-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/92f70397-36e9-46fd-8823-6866eb1ee729/ASAP-overview-twitter.jpeg News - NIH awards initial $68M for AI-driven Structure-enabled Antiviral Platform (ASAP) for open science discovery of oral antivirals for pandemic preparedness - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/4/29/iclr-machine-learning-for-drug-discovery-mldd-workshop-talk-slides monthly 0.5 2022-04-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/953a5c56-6ff8-48b1-a1ab-d246aac9c3ec/ICML-MLDD+thumbnail.jpg News - ICLR Machine Learning for Drug Discovery (MLDD) Workshop talk slides - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/3/21/kate-holloway-award-symposium-talk monthly 0.5 2022-03-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/33ea86dd-edd6-447d-b294-fd768a0b51dd/Holloway_Kate_2016_A.jpeg News - Kate Holloway award symposium talk - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/3/24/openeye-cup-xxi-talk-a-moonshot-on-theory-and-practice monthly 0.5 2022-03-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/a55192c8-9066-42a7-95cc-5c966620f88e/CUP+XXI.jpeg News - OpenEye CUP XXI talk - A Moonshot on Theory and Practice - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2022/2/21/nih-bisti-talk monthly 0.5 2022-02-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/e4354b27-dd78-4192-8ce0-74d4a1834f20/thumbnail.jpg News - NIH BISTI talk: Open science antiviral discovery with 
the covid moonshot 
and the open source drug discovery ecosystem - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2021/12/8/university-of-toronto-talk-slides monthly 0.5 2021-12-08 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/be0d7754-3e6f-4887-8fb3-13f403a92122/uoft-first-slide.jpg News - University of Toronto talk slides - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2021/10/26/asap-avidd-proposal monthly 0.5 2021-10-28 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1635290922291-URO4W7OWX88RGG65P3EX/image1.png News - COVID Moonshot proposes new Antiviral Drug Discovery (AViDD) Center embracing open science and open-IP for global, equitable access - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1635292321808-MY9XJV8DMFU5XWNHRTIU/sars-mers-covid.jpg News - COVID Moonshot proposes new Antiviral Drug Discovery (AViDD) Center embracing open science and open-IP for global, equitable access - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1635291497501-GQ9J81CT33LTQ8U8PRTS/knowable-magazine.jpg News - COVID Moonshot proposes new Antiviral Drug Discovery (AViDD) Center embracing open science and open-IP for global, equitable access - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1635291137743-ZD8PLVRDUXKHR1XCMW8F/ASAP-overview-twitter.jpg News - COVID Moonshot proposes new Antiviral Drug Discovery (AViDD) Center embracing open science and open-IP for global, equitable access - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/openmm-nih-grant-awarded monthly 0.5 2021-07-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1626369849910-RC3OJCGOAKGYMVX8P16Z/nigms-logo.jpeg News - OpenMM secures federal funding though an NIH NIGMS R01 grant - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/news/2021/4/5/acs-spring-2021-national-meeting-a-call-to-action-the-many-roles-of-computational-chemistry-in-addressing-covid-19 monthly 0.5 2021-04-05 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1617664544736-8S1RBHMFB76TV36UJNIH/acs-thumbnail.jpg News - ACS Spring 2021 National Meeting: A Call to Action: The Many Roles of Computational Chemistry in Addressing COVID-19 https://www.choderalab.org/news/2021/4/1/oxford-centre-for-medicines-discovery-talk monthly 0.5 2021-04-01 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1617253943408-AXH2U9KYXL3HI0F03XFW/2021-03-31%C2%A0Oxford%C2%A0Centre%C2%A0for%C2%A0Medicines%C2%A0Discovery+-+thumnbnail.jpg News - Oxford Centre for Medicines Discovery talk https://www.choderalab.org/news/2021/3/16/covid-moonshot-update-at-winter-rosettacon monthly 0.5 2021-03-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1615938030360-RJGDZ1Z9MAQ2120GHEL0/rosettacon-thumbnail.jpg News - COVID Moonshot update at Winter RosettaCon https://www.choderalab.org/news/2021/2/22/covid-moonshot-update-at-the-biophysical-society-annual-meeting-protein-small-molecule-interactions-session monthly 0.5 2021-02-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1613976650540-O5BYY32UNM3X6GNH604L/bps-slides.jpg News - COVID Moonshot update at the Biophysical Society Annual Meeting : Protein-small molecule interactions session https://www.choderalab.org/news/covid-moonshot-2021-01-27 monthly 0.5 2021-01-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1611772374054-OAA9R7Z1PRNFJQ4MCXJF/thumbnail.jpg News - Update on the COVID Moonshot for COVID/SARS CoV2 Rapid Research Reports #5 https://www.choderalab.org/news/neurips-2020 monthly 0.5 2020-11-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1606616544845-4828X1YZ6671M7QB2HPV/neurips-talk-graphic.jpg News - NeurIPS 2020 talk https://www.choderalab.org/news/2020/11/19/foldinghome-20th-anniversary-livestream monthly 0.5 2020-11-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1605833092922-IYLZ3HSV5FDRXYXKOIKA/foldingathome-20th-anniversary-livestream.jpg News - Folding@home 20th Anniversary Livestream! https://www.choderalab.org/news/2020/10/15/help-us-secure-federal-funding-for-openmm monthly 0.5 2020-11-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1602739571040-CRURRXP5WP72HZ72M9Z2/qml-mm.jpg News - Help us secure federal funding for OpenMM! https://www.choderalab.org/news/covid-moonshot-nih-proposal monthly 0.5 2021-02-01 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594518451260-KS4XVF878ABYSTUKSR40/covid-moonshot-logo-small.jpg News - COVID Moonshot seeks NIH funding https://www.choderalab.org/news/2020/4/9/slides-from-covid-moonshot-biosolveit-webinar monthly 0.5 2020-04-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1586446483574-FH4TH91RTLP7NDRGBWQW/biosolve-it-webinar.jpg News - Slides from COVID Moonshot BioSolveIT Webinar https://www.choderalab.org/news/2020-02-05-openmm-r01-submission monthly 0.5 2020-02-09 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1581254072429-7JP1IUHDIJI0I8RSUH22/openmm-logo.jpg News - Securing sustainable funding to enable OpenMM to continue to power the next decade in biomolecular modeling and simulation https://www.choderalab.org/news/labsgiving-2019 monthly 0.5 2019-11-28 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1574969007068-O830HTZRS58C20PQ8YG8/labsgiving-1.jpeg News - Slides from Labsgiving group meeting on software development best practices https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1574969605263-Y9R24FE85OQOY5ZG2CK5/PANO_20191126_103954.vr+%281%29.jpg News - Slides from Labsgiving group meeting on software development best practices https://www.choderalab.org/news/molssi-ml-in-chemistry-2019 monthly 0.5 2019-11-17 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1574021917637-DY9ZRUBBRVITHS3V15QT/slide+thumbnail.jpg News - Slides from John Chodera's talk at MolSSI Workshop on Machine Learning in Chemistry https://www.choderalab.org/news/gcc-2019 monthly 0.5 2019-11-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1573029831494-MYNXGCMN793XCL0Q9ALL/2019-11-05+GCC+talk+intro+slide.png News - Slides from John Chodera's talk at GCC 2019 https://www.choderalab.org/news/cadd-grc-2019 monthly 0.5 2019-11-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1563225769507-9A6ZJ8799W1HP5MN17FM/image-asset.png News - Slides from the 2019 CADD GRC meeting in Mount Snow, VT https://www.choderalab.org/news/2019/5/9/slides-from-john-choderas-keynote-at-the-nyc-maccnyagim-symposium monthly 0.5 2019-11-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1557426788274-LCK4P8KRYF2S875H1Z0O/first-slide.jpg News - Slides from John Chodera's keynote talk at the NYC MACC/NYAGIM Symposium https://www.choderalab.org/news/2018/10/20/the-chodera-lab-teams-up-with-andrea-volkamer-to-explore-the-interface-of-machine-learning-and-free-energy-calculations monthly 0.5 2018-10-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1540049744725-5M77S0TS90JTSOXRYO7U/andrea-volkamer.jpg News - The Chodera lab teams up with Andrea Volkamer to explore the interface of machine learning and free energy calculations Professor Andrea Volkamer, Charité (Berlin) works at the frontier of structure-guided machine learning for drug discovery and kinase inhibition. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1540049660366-AQXXRYOAAROQBOIWL764/ml-workflow.png News - The Chodera lab teams up with Andrea Volkamer to explore the interface of machine learning and free energy calculations An example workflow for utilizing structure-informed machine learning and free energy calculations to predict kinase polypharmacology. https://www.choderalab.org/news/2018/10/20/celebrating-six-years-of-the-chodera-lab monthly 0.5 2020-06-11 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1540048395876-X5MO3LVK8SHFIIRGSKDX/screenshot.png News - Celebrating six years of the Chodera lab! https://www.choderalab.org/news/2018/7/4/congratulations-to-tpcb-graduate-student-chaya-stern-for-being-selected-for-a-2018-molssi-phase-i-fellowship monthly 0.5 2018-07-04 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1530721125333-RM5V59ZJVDIHB7O8H97U/Chaya+Stern.jpg News - Congratulations to TPCB graduate student Chaya Stern for being selected for a 2018 MolSSI Phase I Fellowship! https://www.choderalab.org/news/2018/7/4/2018-workshop-on-free-energy-methods-kinetics-and-markov-state-models-in-drug-design-videos-are-up monthly 0.5 2018-07-04 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1530723025790-AUDFM57AUH4L2EUSL8Z3/drugmsm.jpg News - 2018 Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design: Videos are up! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1530722885174-EUDMOG795ZEV4OMK8M8I/drugalchemy.jpg News - 2018 Workshop on Free Energy Methods, Kinetics and Markov State Models in Drug Design: Videos are up! https://www.choderalab.org/news/2018/4/21/seeking-a-joint-open-force-field-consortium-xtalpi-distinguished-postdoctoral-fellow monthly 0.5 2018-04-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1524346977001-3NS01XFV2PU8WGENMOSE/OFFC-XTALPI.png News - Seeking a joint Open Force Field Consortium / XtalPi Distinguished Postdoctoral Fellow https://www.choderalab.org/news/2018/3/12/additional-reading-for-mskcc-responsible-conduct-of-research monthly 0.5 2018-03-13 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1520905912013-NUJ67XL9LV5H3D4NSWAT/NIH-Logo.gif News - Additional reading for MSKCC Responsible Conduct of Research https://www.choderalab.org/news/2018/2/22/sampl6-overview-slides monthly 0.5 2018-02-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1519336038266-L9Z048XCQIJ6TFTKNHQR/d3r-location.jpg News - SAMPL6 overview slides https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1519335851117-SQ2KC6FIZHM4J8V0479N/sampl6-overview-slides.png News - SAMPL6 overview slides https://www.choderalab.org/news/2018/1/23/the-open-forcefield-consortium-seeks-a-software-scientist monthly 0.5 2018-01-23 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1516734364997-00Q7DO4TA3IR0E96F68B/smirks_direct-768x495+%281%29.jpg News - The Open Forcefield Consortium seeks a software scientist https://www.choderalab.org/news/2018/2/18/sonya-hanson-joins-nobel-laureate-joachim-franks-lab monthly 0.5 2018-02-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1519243202728-O0PMTPRG69GM8N0OBIDT/Hanson_171003_06.jpg News - Postdoc Sonya Hanson joins Nobel Laureate Joachim Frank's lab https://www.choderalab.org/news/2018/1/23/postdoc-gregory-ross-joins-schrdinger-as-a-senior-scientist monthly 0.5 2018-01-23 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1516733315024-YH2B9PGHEP65YVJCTXRP/gregory_ross.jpeg News - Postdoc Gregory Ross joins Schrödinger as a Senior Scientist https://www.choderalab.org/news/2017/11/9/openeye-minicup-boston-building-next-generation-forcefields-and-moving-free-energy-calculations-to-the-cloud monthly 0.5 2017-11-09 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1510240230384-V8FTI4GNZ1YMPF45ZGOP/logo.jpg News - OpenEye MiniCUP Boston: Building next-generation forcefields and moving free energy calculations to the cloud https://www.choderalab.org/news/2017/9/29/chodera-lab-awarded-nih-r01-to-study-role-of-conformational-reorganization-energy-in-selective-kinase-inhibition monthly 0.5 2017-09-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1506728641838-D9TGLQPSYHVJ83Z43SP5/nih-logo.jpg News - Chodera lab awarded NIH R01 to study role of conformational reorganization energy in selective kinase inhibition https://www.choderalab.org/news/2017/9/29/chodera-lab-awarded-nsf-grant-to-study-new-techniques-for-bayesian-forcefield-parameterization monthly 0.5 2017-09-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1506729353475-FWO2CNH7WV5RXD8PXANR/nsf-logo.jpg News - Chodera lab awarded NSF grant to study new techniques for Bayesian forcefield parameterization https://www.choderalab.org/news/2017/7/14/slides-from-the-2017-telluride-free-energy-meeting monthly 0.5 2017-07-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1500052897619-VCTNBKTI0TP14E5JCY4W/IMG_6921.JPG News - Slides from the 2017 Telluride Free Energy Meeting https://www.choderalab.org/news/2017/6/30/stop-fighting-matplotlib-and-make-it-do-what-you-want monthly 0.5 2017-06-30 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1498865341129-254OK7HHIBP1ZB2U8U58/image-asset.jpeg News - Stop fighting matplotlib and make it do what you want https://www.choderalab.org/news/2017/6/1/congratulations-to-rafal-wiewiora-on-receiving-a-cancer-research-horizon-award monthly 0.5 2017-06-01 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1496356791372-IHT9MBXDOOWORY37XXH2/image-asset.jpeg News - Congratulations to Rafal Wiewiora on receiving a Cancer Research Horizon Award! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1496356899828-ZUI1SJ0G1F6JCPQNJ4IG/dod_figure.jpg News - Congratulations to Rafal Wiewiora on receiving a Cancer Research Horizon Award! Combined computational and experimental approach to discovering selective inhibitors of EZH2 and SETDB1 that exploit differences in conformational reorganization energies to achieve selectivity. https://www.choderalab.org/news/2017/6/29/congratulations-to-patrick-grinaway-on-being-funded-by-an-open-science-fellowship-from-silicon-therapeutics monthly 0.5 2017-06-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1498746387461-DEAPPMZRCUXLYAT9FOB6/image-asset.jpeg News - Congratulations to Patrick Grinaway on being funded by an Open Science Fellowship from Silicon Therapeutics! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1498746446438-YQ07CJZI0LAY24OQHH9V/image-asset.png News - Congratulations to Patrick Grinaway on being funded by an Open Science Fellowship from Silicon Therapeutics! https://www.choderalab.org/news/2017/5/22/congratulations-to-chaya-stern-for-receiving-a-diversity-scholarship-to-attend-scipy-2017 monthly 0.5 2017-05-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1495484103189-8Y64MK9EN863XS5ZFOIZ/SciPy2017-Logo-NoTag-12.16.16.png News - Congratulations to Chaya Stern for receiving a Diversity Scholarship to attend SciPy 2017! https://www.choderalab.org/news/2017/4/20/greg-ross-molssi-fellowship monthly 0.5 2017-04-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1492720735165-6TJIP09WT9HP3X8GX00R/gregory-ross.jpeg News - Postdoc Gregory Ross awarded Postdoctoral MolSSI Fellowship https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1492714378002-PUG0TJ6HYZPFRE9567DT/image-asset.png News - Postdoc Gregory Ross awarded Postdoctoral MolSSI Fellowship https://www.choderalab.org/news/2017/3/27/congratulations-to-tpcb-graduate-student-mehtap-isik-on-being-awarded-the-2017-2018-doris-j-hutchison-fellowship monthly 0.5 2017-03-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1490641192574-XPFOM13IFH8UQSNA0MXD/image-asset.jpeg News - Congratulations to TPCB graduate student Mehtap Isik on being awarded the 2017-2018 Doris J. Hutchison Fellowship https://www.choderalab.org/news/2017/3/12/nature-chemical-biology-paper-about-ldha-alternative-substrate-utilization-at-low-ph-is-out monthly 0.5 2017-03-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1489360420376-IHK3TC5MS5MBBRO0LQEZ/image-asset.png News - Nature Chemical Biology paper about LDHA alternative substrate utilization at low pH is out! https://www.choderalab.org/news/2017/3/8/cup-xvii-slides monthly 0.5 2017-03-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1489359944907-ZRJK9YZ1CN9BH2BGNED5/image-asset.png News - CUP XVII talk slides https://www.choderalab.org/news/2017/2/14/harvard-widely-applied-mathematics-talk-slides monthly 0.5 2017-03-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1487077729568-HDD3AI4NH3WSVUZXBZJE/image-asset.gif News - Harvard Widely Applied Mathematics talk slides https://www.choderalab.org/news/2017/2/6/new-nature-chemical-biology-paper-on-aurora-a-kinase-a-potential-melanoma-target monthly 0.5 2017-02-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1486428788533-JNFMMT73RC75BAEUTTZ4/image-asset.jpeg News - New Nature Chemical Biology paper on Aurora A kinase, a potential melanoma target https://www.choderalab.org/news/2016/12/26/microsecond-trajectory-of-human-tyrosine-kinase-abl1-kinase-domain-on-figshare monthly 0.5 2016-12-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482781516428-84P6RWYW9AAQQIS686E0/image-asset.jpeg News - Microsecond trajectory of human tyrosine kinase ABL1 kinase domain on Figshare https://www.choderalab.org/news/2016/12/26/openmm-71-beta-released monthly 0.5 2016-12-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482781384054-MOUYU3XKME4PMD7B11AF/image-asset.png News - OpenMM 7.1 beta released https://www.choderalab.org/news/2016/12/17/slides-for-gsk-visit monthly 0.5 2016-12-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482032763350-KYD43YYR4NRD4DB85C5V/image-asset.jpeg News - Slides for GSK visit https://www.choderalab.org/news/2016/12/17/human-kinase-domain-constructs-kit-featured-by-addgene monthly 0.5 2016-12-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482033935493-OBOKMDSBQ6RE7WM4X64Z/image-asset.png News - Human kinase domain constructs kit featured by AddGene https://www.choderalab.org/news/2016/12/17/response-to-nih-rfi-on-preprints monthly 0.5 2016-12-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482034445556-GFKDBYL1ZLS7FG0A1BW8/i-post-preprints.png News - Response to NIH RFI on preprints Credit: Jessica Polka, ASAPbio https://www.choderalab.org/news/2016/11/12/help-us-reach-one-million-volunteers-to-foldinghome monthly 0.5 2016-11-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1478985915123-6GSLDV669NCBZSI8NS10/image-asset.jpeg News - Help us reach one million folders on Folding@home! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1478986521381-Q6Z66A2SIZU32IWNGG22/image-asset.png News - Help us reach one million folders on Folding@home! https://www.choderalab.org/news/2016/9/14/slides-for-ccpbiosim-talk-at-kings-college-london monthly 0.5 2016-09-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1473859871751-UG5LFT8JARHL78W2H66G/image-asset.jpeg News - Slides for CCPBioSim talk at Kings College London https://www.choderalab.org/news/2016/8/23/acs-philadelphia-polypharmacology-session-slides monthly 0.5 2016-08-23 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1471973902981-4EJ7FHKZKLAMOLYNA2T0/image-asset.jpeg News - ACS Philadelphia Polypharmacology session slides https://www.choderalab.org/news/2016/8/22/acs-session-on-sharing-pharmaceutical-industry-data monthly 0.5 2016-08-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1471894929990-NKCI2DD9I06R5YPEI8MC/image-asset.jpeg News - ACS Session on Sharing Pharmaceutical Industry Data https://www.choderalab.org/news/2016/7/29/blog monthly 0.5 2016-07-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1469788394992-LN0RBRQKV0T6LEU6S844/image-asset.jpeg News - Blog! https://www.choderalab.org/news/2016/5/17/fourth-alchemical-free-energy-calculations-in-drug-design-meeting-at-vertex monthly 0.5 2016-05-17 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1463511102314-I9N0VY54RLRHFD9A16G4/image-asset.jpeg News - Fourth Alchemical Free Energy Calculations in Drug Design meeting at Vertex https://www.choderalab.org/news/2016/3/22/6hp6c2fg6zxile8g3lhlkgf1uum0wo monthly 0.5 2016-03-28 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1458707677223-VGNB2HWRBV3FZ47R1LP9/image-asset.jpeg News - Genspace NYC: Slides from postdoc Dr Sonya Hanson https://www.choderalab.org/news/2016/3/16/acs-san-diego-real-w monthly 0.5 2016-03-16 https://www.choderalab.org/news/2016/3/7/icms-edinburgh-workshop-on-multiscale-methods-for-stochastic-dynamical-systems-in-biology monthly 0.5 2016-03-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1457356459319-NADVYLV5Z9BWAC7I6TUA/IMG_8566.JPG News - ICMS Edinburgh Workshop on multiscale methods for stochastic dynamical systems in biology https://www.choderalab.org/news/2016/3/3/gtc-11th-meetig-on-kinases-in-drug-discovery monthly 0.5 2016-03-03 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1457015352956-MXPVWVV6GHZGAJNF0YR8/image-asset.jpeg News - GTC 11th Meeting on Kinases in Drug Discovery https://www.choderalab.org/news/2015/10/29/talk-slides-for-autodesk-bionano-talk monthly 0.5 2015-10-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1446139365330-WODQLWDI8O4YUO81DIXJ/image-asset.jpeg News - Talk slides for Autodesk Bio/Nano talk https://www.choderalab.org/news/2015/10/19/cecam-workshop-on-developing-interoperable-and-portable-molecular-simulation-software-libraries monthly 0.5 2015-10-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1445240368112-H2E6V9QS8DPOZXQ70YRS/image-asset.png News - CECAM Workshop on developing interoperable and portable molecular simulation software libraries https://www.choderalab.org/news/2015/7/20/posters-from-the-computer-aided-drug-discovery-cadd-grc monthly 0.5 2015-08-03 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1437439557141-L6VCE9OZOQQJC4AM53UU/image-asset.jpeg News - Posters from the Computer Aided Drug Discovery (CADD) GRC https://www.choderalab.org/news/2015/6/26/science-communication-boot-camp-the-experience monthly 0.5 2015-07-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435808977375-Q80Y5OCZ1DUEVGILC1AV/image-asset.jpeg News - Science Communication Boot Camp: The Experience https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435809843304-V8OLBW5R4PO0UJYXN2ZA/image-asset.png News - Science Communication Boot Camp: The Experience https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435808928096-WD985GTOPZKM40VUA7JI/image-asset.gif News - Science Communication Boot Camp: The Experience https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435809197326-O5KCSKDJ20IJ4IMQHKQJ/image-asset.jpeg News - Science Communication Boot Camp: The Experience https://www.choderalab.org/news/2015/6/30/automatic-equilibration-detection-manuscript-on-biorxiv monthly 0.5 2015-07-05 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435678098461-OH07A5MB2718TVEYNB65/image-asset.jpeg News - Automatic equilibration detection manuscript on bioRxiv https://www.choderalab.org/news/2015/6/14/science-communication-bootcamp monthly 0.5 2015-06-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1434303005452-00FBV8P7ESEW0FZQN562/image-asset.jpeg News - Postdoc Sonya Hanson participates in inaugural Alan Alda Center for Communicating Science Summer Bootcamp https://www.choderalab.org/news/2015/6/12/automated-forcefield-benchmarking-manuscript-on-arxiv monthly 0.5 2015-06-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1434129550303-H28LYY7KYE0L0R3ADPXB/liquid-benchmark.png News - Automated forcefield benchmarking manuscript on arXiv https://www.choderalab.org/news/2015/6/4/openeye-jcup-vi-talk-slides monthly 0.5 2015-06-05 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1433464570766-OPR462JM1IWFGB2CDXNW/JDC-JCUP-VI-badge.jpg News - OpenEye JCUP VI talk slides https://www.choderalab.org/news/2015/5/21/kinase-inhibitor-dorm-room-poster monthly 0.5 2015-06-01 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1432235666443-75NYIREVFFZRYTEZ44KR/image-asset.png News - Kinase Inhibitor Dorm Room Poster! https://www.choderalab.org/news/2015/4/15/chaya-stern-awarded-nsf-graduate-fellowship monthly 0.5 2015-04-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1429154295915-AY2V2XLKA8SPLR0XRM8U/image-asset.png News - Chaya Stern awarded NSF Graduate Fellowship https://www.choderalab.org/news/2015/4/15/ensembler-paper-on-bioarxiv monthly 0.5 2015-04-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1429140054057-DHEF8KHR554WXFHAYF01/image-asset.jpeg News - Ensembler paper on biorXiv https://www.choderalab.org/news/2015/3/30/chodera-lab-seeking-awesome-tech-to-help-advance-drug-discovery-science-with-robots-and-gpus monthly 0.5 2019-03-03 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762006828-R8VIG4ZH347LXRXMV6ZK/IMG_0006.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762006832-DCRV1PR0623OSDN3BYIX/IMG_3158.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762006927-DAHO0AKGI0ZKKOD9557M/IMG_3267.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762006961-6MD20NTBEL3HGEG8O61D/IMG_3268.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007011-6FZ9UQWDM7J9M4FX1NC2/IMG_3333.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007047-ADA12AE6D4WNHL9BIEFC/IMG_3336.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007135-P10ED8M1ALAZVUO0QF9T/IMG_3337.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007272-9EV46TOHRXAWFWLJKYGX/IMG_3338.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007362-UA0B4CC0TWG4R8UV81C4/IMG_3339.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007364-ERW55N97E6GEHYQUD5OR/IMG_3340.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007438-BRHC406Y1TYD7XGYJ6CW/IMG_3341.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007574-DXN3UTOD8OANULVYDFMG/IMG_3342.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1427762007553-QMLA4RZ2JR553XI6910G/IMG_3349.jpg News - Chodera lab seeking awesome tech to help advance drug discovery science with robots and Python! https://www.choderalab.org/news/2015/2/24/congratulations-and-farewell-to-postdoc-jan-hendrik-prinz monthly 0.5 2015-02-24 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1424783469957-S50MKD41PBXW461HPZ5J/image-asset.jpeg News - Congratulations and farewell to postdoc Jan-Hendrik Prinz https://www.choderalab.org/news/2015/2/10/biophysical-society-update-talks-and-blogging monthly 0.5 2015-02-12 https://www.choderalab.org/news/2015/2/6/the-chodera-lab-is-headed-to-the-biophysical-society-meeting-in-baltimore-feb-7-11 monthly 0.5 2015-02-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1423254638004-O0V3956ZNDXL73BFF7CJ/image-asset.jpeg News - The Chodera lab is headed to the Biophysical Society Meeting in Baltimore https://www.choderalab.org/news/2015/1/27/talk-slides-for-new-york-structural-biology-discussion-group-nysbdg-posted monthly 0.5 2015-01-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1422379913343-YD81HE02U88PLR02A5HV/image-asset.jpeg News - Talk slides for New York Structural Biology Discussion Group (NYSBDG) posted https://www.choderalab.org/news/2015/1/27/the-chodera-lab-is-profiled-in-this-weeks-genomeweb monthly 0.5 2015-01-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1422379166255-AZN3R6B2W4IERDMM0HDD/image-asset.png News - The Chodera lab is profiled in this week's GenomeWeb https://www.choderalab.org/news/2015/1/14/foldinghome-comes-to-sony-android-phones monthly 0.5 2015-01-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1421254507386-J2N57W2AAK1PC4VFJA8J/foldingathome-sony-android.png News - Folding@home comes to Sony Android phones! 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The empty half of the bay, prepared to receive automation equipment. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1396116665244-U8YIIGMKBI0C2221FPTB/image-asset.png News - And so it begins... 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0.5 https://www.choderalab.org/news/tag/visit monthly 0.5 https://www.choderalab.org/news/tag/COVID+Moonshot monthly 0.5 https://www.choderalab.org/news/tag/NeurIPS monthly 0.5 https://www.choderalab.org/news/tag/ASAP monthly 0.5 https://www.choderalab.org/publications daily 0.75 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1393711464659-SNPQ0OEBL4CZOYGNH1NM/src-imatinib-1040.jpg Publications https://www.choderalab.org/publications/2024/12/24/prospective-evaluation-of-structure-based-simulations-reveal-their-ability-to-predict-the-impact-of-kinase-mutations-on-inhibitor-binding monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/a8e3eb97-2739-4866-b0ba-435a5f4f89fd/prospective-kinase-mutations.jpg Publications - Prospective evaluation of structure-based simulations reveal their ability to predict the impact of kinase mutations on inhibitor binding - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/12/25/nutmeg-and-spice-models-and-data-for-biomolecular-machine-learning monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/533f799b-90c3-4dd0-8067-24c73b586599/nutmeg-spice.jpg Publications - Nutmeg and SPICE: Models and data for biomolecular machine learning - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/12/25/lessons-learned-during-the-journey-of-data-from-experiment-to-model-for-predicting-kinase-affinity-selectivity-polypharmacology-and-resistance monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/d7ff84b2-d5a0-4331-ad38-c6cd90088647/kinoml-lessons-learned.jpg Publications - Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/machine-learned-molecular-mechanics-force-field-for-the-simulation-of-protein-ligand-systems-and-beyond monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/c0d9f750-2bcf-497b-96e9-bfed236c61c8/espaloma-0.3.jpg Publications - Machine-learned molecular mechanics force fields from large-scale quantum chemical data - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/12/25/druggym-a-testbed-for-the-economics-of-autonomous-drug-discovery monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/0989d587-2574-497c-a487-3f1a6ca1ee52/drug-gym.jpg Publications - DrugGym: A testbed for the economics of autonomous drug discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/12/25/enhancing-proteinligand-binding-affinity-predictions-using-neural-network-potentials monthly 0.5 2024-12-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1a22d748-6750-415e-9b25-4282ffa0386b/de-fabritiis-nnp-free-energy.jpg Publications - Enhancing protein–ligand binding affinity predictions using neural network potentials - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/death-by-a-thousand-cuts-combining-kinase-inhibitors-for-selective-target-inhibition-and-rational-polypharmacology monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/f14c9708-8f6c-4581-adbb-d30a913e9192/multicompound-multitarget-scoring.jpg Publications - Death by a thousand cuts through kinase inhibitor combinations that maximize selectivity and enable rational multitargeting - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/openmm-8-molecular-dynamics-simulation-with-machine-learning-potentials monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/ed3b88ed-bf4e-4452-94f5-2ed4ce2a2d6c/openmm7-logo.jpg Publications - OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/open-science-discovery-of-potent-noncovalent-sars-cov-2-main-protease-inhibitors monthly 0.5 2024-10-23 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/181bdc4b-d56e-4e60-b1b5-71d83b2195f1/covid-moonshot-logo-small.jpg Publications - Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/benchmarking-cross-docking-strategies-for-structure-informed-machine-learning-in-kinase-drug-discovery monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/2e86caca-c247-4800-86f2-9bdb92980ad8/kinase-docking.jpg Publications - Benchmarking cross-docking strategies for structure-informed machine learning in kinase drug discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/nnpmm-fast-molecular-dynamics-simulations-with-machine-learning-potentials-and-molecular-mechanics monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/8a6338a1-5a79-4f24-b061-d7d32daaedf3/nnp-mm.jpg Publications - NNP/MM: Fast molecular dynamics simulations with machine learning potentials and molecular mechanics - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/identifying-and-overcoming-the-sampling-challenges-in-relative-binding-free-energy-calculations-of-a-model-proteinprotein-complex monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/73f119d3-3a0e-45c3-8ea3-1331f04a9528/mutations.jpg Publications - Identifying and Overcoming the Sampling Challenges in Relative Binding Free Energy Calculations of a Model Protein:Protein Complex - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/development-and-benchmarking-of-open-force-field-200-the-sage-small-molecule-force-field monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/258d2a92-cc0d-4859-bc6d-82e47a0546d6/sage.jpg Publications - Development and benchmarking of Open Force Field 2.0.0---the Sage small molecule force field - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/men1-mutations-mediate-clinical-resistance-to-menin-inhibition monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/cafcdb57-716f-4062-9c44-1c3332feeaf8/men1.jpg Publications - MEN1 mutations mediate clinical resistance to menin inhibition - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/turning-high-throughput-structural-biology-into-predictive-inhibitor-design monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/0706a4ef-68b6-40c8-8b63-7cc7a9b40a1d/kadi-fragments.jpg Publications - Turning high-throughput structural biology into predictive inhibitor design - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/espalomacharge-machine-learning-enabled-ultra-fast-partial-charge-assignment monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/b5f4bf5a-2d43-4fa8-b4c7-346094df216c/espaloma-charge.jpg Publications - EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/24/spatial-attention-kinetic-network-with-en-equivariance monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/d0c4fe8e-e912-4eea-88ad-23ea93359742/sake-thumbnail.png Publications - Spatial attention kinetic network with E(n) equivariance - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2024/1/21/spice-a-dataset-of-drug-like-molecules-and-peptides-for-training-machine-learning-potentials monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/2e4032f3-fa88-4571-bcce-241837ee1ea7/spice-dataset.jpg Publications - SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/open-force-field-bespokefit-automating-bespoke-torsion-parametrization-at-scale monthly 0.5 2024-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/99053f1e-ee17-4f99-884e-2ddfb4de366a/bespokefit.jpg Publications - Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2020/10/6/end-to-end-differentiable-molecular-mechanics-force-field-construction monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1633529664420-3U4TUSYFU6U9577UO5OY/espaloma_visual_abstract.png Publications - End-to-end differentiable molecular mechanics force field construction https://www.choderalab.org/publications/2023/1/22/improving-force-field-accuracy-by-training-against-condensed-phase-mixture-properties monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/2bc9595d-a670-4a18-99f4-3cf4da113b41/openff-evaluator.jpg Publications - Improving force field accuracy by training against condensed-phase mixture properties - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/sampl7-protein-ligand-challenge-a-community-wide-evaluation-of-computational-methods-against-fragment-screening-and-pose-prediction monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/8a601584-6826-4038-bbdc-bb755e3a294b/sampl7-phip2.jpg Publications - SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/cache-critical-assessment-of-computational-hit-finding-experiments-a-public-private-partnership-benchmarking-initiative-to-enable-the-development-of-computational-methods-for-hit-finding monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/a7a32494-08a1-4606-a97d-e9a934cd0b1e/cache.jpg Publications - CACHE (Critical Assessment of Computational Hit-finding Experiments): A public-private partnership benchmarking initiative to enable the development of computational methods for hit-finding - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/ink4-tumor-suppressor-proteins-mediate-resistance-to-cdk46-kinase-inhibitors monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/3556bb12-72c7-4139-b0b4-c163eb3a2d39/ink4-cdk4.jpg Publications - INK4 tumor suppressor proteins mediate resistance to CDK4/6 kinase inhibitors - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/capturing-non-local-through-bond-effects-in-molecular-mechanics-force-fields-ii-using-fractional-bond-orders-to-fit-torsion-parameters monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/fb0230f9-e4bb-47e2-b9b4-7af8f87f04a8/biphenyl-wbo.jpg Publications - Capturing non-local through-bond effects in molecular mechanics force fields: II. Using fractional bond orders to fit torsion parameters - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/gcn2-kinase-activation-by-atp-competitive-kinase-inhibitors monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/22f99055-f958-4ae6-96d6-8fa9af881712/gcn2-activation.jpg Publications - GCN2 kinase activation by ATP-competitive kinase inhibitors - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2023/1/22/quantum-chemistry-common-driver-and-databases-qcdb-and-quantum-chemistry-engine-qcengine-automation-and-interoperability-among-computational-chemistry-programs monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/6d675d51-c2f7-4d19-a5e4-729c6247abb6/qcarchive.jpg Publications - Quantum chemistry common driver and databases (QCDB) and quantum chemistry engine (QCEngine): Automation and interoperability among computational chemistry programs - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/9/6/teaching-free-energy-calculations-to-learn-from-experimental-data monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1630959591879-4KC1R33JDD1EDYUOK793/qml-explicit-free-energy.jpg Publications - Teaching free energy calculations to learn from experimental data - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/8/30/the-open-force-field-evaluator-an-automated-efficient-and-scalable-framework-for-the-estimation-of-physical-properties-from-molecular-simulation monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1630300709382-WFBGYZW1YWE5GE78YEDH/openff-evaluator.jpg Publications - The Open Force Field Evaluator: An automated, efficient, and scalable framework for the estimation of physical properties from molecular simulation - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/6/antibodies-to-the-sars-cov-2-receptor-binding-domain-that-maximize-breadth-and-resistance-to-viral-escape monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625622430276-GBVQWD6L4EB9IFEJBTPT/vir-antibodies-escape.jpg Publications - Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/5/mutation-in-abl-kinase-with-altered-drug-binding-kinetics-indicates-a-novel-mechanism-of-imatinib-resistance monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625466464720-66WS08O075KU2IB9VVNH/abl-mutant-kinetics.jpg Publications - Mutation in Abl kinase with altered drug binding kinetics indicates a novel mechanism of imatinib resistance - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/4/a-white-knuckle-ride-of-open-covid-drug-discovery monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625455379877-LZIDWY7HQ73G999S9Q9F/covid-moonshot-nature-commentary.jpg Publications - A white-knuckle ride of open COVID drug discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/5/best-practices-for-constructing-preparing-and-evaluating-protein-ligand-binding-affinity-benchmarks monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625459803644-4L0DZG5FP9QN4AQWCPJ3/affinity-benchmark-best-practices.jpg Publications - Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2020/7/5/citizen-scientists-create-an-exascale-computer-to-combat-covid-19 monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594006410839-EZS612JEH04ROIFJY9SN/foldingathome-covid-cryptic-pockets.jpg Publications - SARS-CoV-2 simulations go exascale to predict dramatic spike opening and cryptic pockets across the proteome https://www.choderalab.org/publications/2021/7/5/bayesian-inference-driven-model-parameterization-and-model-selection-for-2cljq-fluid-models monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625457604190-13MBIRN9QZWYJ52XZYOR/2CLJQ.jpg Publications - Bayesian inference-driven model parameterization and model selection for 2CLJQ fluid models - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/6/discovery-of-sars-cov-2-main-protease-inhibitors-using-a-synthesis-directed-de-novo-design-model monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625620876650-7BQ6XX14ZRBTWZLGXNFO/postera-ml-model.jpg Publications - Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/5/what-markov-state-models-can-and-cannot-do-correlation-versus-path-based-observables-in-protein-folding-models monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625462741743-3M65NAE97NN8ZTMRMHDV/what-can-msms-do.jpg Publications - What Markov State Models can and cannot do: Correlation versus path-based observables in protein-folding models - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/2/7/circulating-sars-cov-2-spike-n439k-variants-maintain-fitness-while-evading-antibody-mediated-immunity monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1612757912797-WXMV7778MZHPTE6BP4AF/vir-cell-xray.jpg Publications - Circulating SARS-CoV-2 spike N439K variants maintain fitness while evading antibody-mediated immunity https://www.choderalab.org/publications/2021/7/5/overview-of-the-sampl6-pka-challenge-evaluating-small-molecule-microscopic-and-macroscopic-pka-predictions monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625465745103-5CMKX4ON40DSQPHSBW69/sampl6-pka-assessment.jpg Publications - Overview of the SAMPL6 pKa challenge: evaluating small molecule microscopic and macroscopic pKa predictions - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2021/7/6/development-and-benchmarking-of-open-force-field-v1-00-the-parsley-small-molecule-force-field monthly 0.5 2021-09-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1625628520558-FHAZ01OBAW39L8QXX8OA/parsley.jpg Publications - Development and benchmarking of Open Force Field v1.0.0, the Parsley small molecule force field - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://www.choderalab.org/publications/2020/11/25/fitting-quantum-machine-learning-potentials-to-experimental-free-energy-data-predicting-tautomer-ratios-in-solution monthly 0.5 2023-01-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1606351509908-J9RXW35NY13FWWB0WIXE/image-asset.png Publications - Fitting quantum machine learning potentials to experimental free energy data: Predicting tautomer ratios in solution https://www.choderalab.org/publications/2020/8/29/capturing-non-local-through-bond-effects-when-fragmenting-molecules-for-quantum-chemical-torsion-scans monthly 0.5 2020-08-29 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1598734849800-WZH8A21EFSM47JRG8SDN/fragmenter.jpg Publications - Capturing non-local through-bond effects when fragmenting molecules for quantum chemical torsion scans https://www.choderalab.org/publications/2020/8/29/best-practices-for-alchemical-free-energy-calculations monthly 0.5 2021-05-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1598751397494-97V1OWYM6M6WQ2X80CZ7/alchemical-best-practices.jpg Publications - Best practices for alchemical free energy calculations https://www.choderalab.org/publications/2020/7/30/towards-chemical-accuracy-for-alchemical-free-energy-calculations-with-hybrid-physics-based-machine-learning-molecular-mechanics-potentials monthly 0.5 2020-07-31 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1596160166910-BFM6HVXM6FDEACH7OFS3/hybrid-qm-mm.jpg Publications - Towards chemical accuracy for alchemical free energy calculations with hybrid physics-based machine learning / molecular mechanics potentials https://www.choderalab.org/publications/2020/7/11/crowdsourcing-drug-discovery-for-pandemics monthly 0.5 2020-07-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594518451260-KS4XVF878ABYSTUKSR40/covid-moonshot-logo-small.jpg Publications - Crowdsourcing drug discovery for pandemics https://www.choderalab.org/publications/2020/7/5/is-structure-based-drug-design-ready-for-selectivity-optimization monthly 0.5 2021-02-08 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594000336176-I3Q7WPHTX24VA6BZXNHB/kinase-selectivity-paper.jpg Publications - Is structure based drug design ready for selectivity optimization? https://www.choderalab.org/publications/2020/8/29/machine-learning-force-fields-and-coarse-grained-variables-in-molecular-dynamics-application-to-materials-and-biological-systems monthly 0.5 2021-02-08 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1598753231118-XAPZNNJ8NIJJL5UPF27X/coarse-graining.jpg Publications - Machine learning force fields and coarse-grained variables in molecular dynamics: application to materials and biological systems https://www.choderalab.org/publications/2020/7/5/standard-state-free-energies-not-pkas-are-ideal-for-describing-small-molecule-protonation-and-tautomeric-states monthly 0.5 2021-02-08 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594004572081-W508X0YPU3SL7CC8EMN6/pka-free-energies.jpg Publications - Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states https://www.choderalab.org/publications/2020/1/31/assessing-the-accuracy-of-octanol-water-partition-coefficient-predictions-in-the-sampl6-part-ii-log-p-challenge monthly 0.5 2020-05-19 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1580508410244-S45KK8CNFH8M0N1V9YL8/sampl6-logP-assessment.png Publications - Assessing the accuracy of octanol-water partition coefficient predictions in the SAMPL6 Part II log P Challenge https://www.choderalab.org/publications/2019/10/10/the-sampl6-sampling-challenge-assessing-the-reliability-and-efficiency-of-binding-free-energy-calculations monthly 0.5 2021-04-21 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1570763155355-BPDKHBYU93AN2HEOWA8F/sampl6-sampling.png Publications - The SAMPL6 SAMPLing challenge: Assessing the reliability and efficiency of binding free energy calculations https://www.choderalab.org/publications/2019/9/5/octanol-water-partition-coefficient-measurements-for-the-sampl6-blind-prediction-challenge monthly 0.5 2021-02-08 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1567701121664-6Z3Q43HA8BHE4QK5P0NV/sampl6-part2-logP.png Publications - Octanol-water partition coefficient measurements for the SAMPL6 Blind Prediction Challenge https://www.choderalab.org/publications/2018/8/25/a-novel-small-molecule-pan-id-antagonist-inhibits-pathologic-ocular-neovascularization monthly 0.5 2020-01-31 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1535238593451-W2W349DC8EP9M6XEADJM/agx51.png Publications - A small-molecule pan-Id antagonist inhibits pathologic ocular neovascularization https://www.choderalab.org/publications/2019/9/17/graph-nets-for-partial-charge-prediction monthly 0.5 2019-09-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1568769476532-IMHUTA1VS6QCRBD0DH87/gimlet.jpg Publications - Graph nets for partial charge prediction https://www.choderalab.org/publications/2019/9/17/sharing-data-from-molecular-simulations monthly 0.5 2020-07-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1594006728302-403T0NEXI57SFYFN0GLJ/sharing-data.gif Publications - Sharing data from molecular simulations https://www.choderalab.org/publications/2019/8/26/ancestral-reconstruction-reveals-mechanisms-of-erk-regulatory-evolution monthly 0.5 2019-10-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1566861236596-9QG6XMBGVKG6E73BOLLZ/erk-reconstruction.jpg Publications - Ancestral reconstruction reveals mechanisms of ERK regulatory evolution https://www.choderalab.org/publications/2019/7/4/binding-thermodynamics-of-host-guest-systems-with-smirnoff99frosst-105-from-the-open-force-field-initiative monthly 0.5 2019-10-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1562263628023-EVQLWEXVAYV1G8T35M7J/smirnoff-vs-gaff.png Publications - Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative https://www.choderalab.org/publications/2018/5/15/small-molecule-targeting-of-musashi-rna-binding-activity-in-acute-myeloid-leukemia monthly 0.5 2019-07-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1526408256196-AJ0V4WW3BKKLA0K9MFNZ/musashi-Ro.png Publications - Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia https://www.choderalab.org/publications/2018/8/20/the-dynamic-conformational-landscapes-of-the-protein-methyltransferase-setd8 monthly 0.5 2019-07-04 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1534817145413-UC73EXRD0C9UZO5SANVG/SETD8-landscape.png Publications - The dynamic conformational landscapes of the protein methyltransferase SETD8 https://www.choderalab.org/publications/2018/4/24/what-makes-a-kinase-promiscuous-for-inhibitors monthly 0.5 2019-07-04 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1524598569463-GHYSCZQUO3ALQW3WAUMN/kinase-promiscuity.jpg Publications - What makes a kinase promiscuous for inhibitors? https://www.choderalab.org/publications/2018/6/21/openpathsampling-a-python-framework-for-path-sampling-simulations-ii-building-and-customizing-path-ensembles-and-sample-schemes monthly 0.5 2019-07-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1529621876812-MSSD0PHP84LFLR64OD78/ops-logo.png Publications - OpenPathSampling: A Python framework for path sampling simulations. II. Building and customizing path ensembles and sample schemes https://www.choderalab.org/publications/2018/6/21/openpathsampling-a-python-framework-for-path-sampling-simulations-i-basics monthly 0.5 2019-07-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1529621296736-TQL74PKIJDGHS425P0P3/ops-logo.png Publications - OpenPathSampling: A Python framework for path sampling simulations. I. Basics https://www.choderalab.org/publications/2018/5/9/toward-learned-chemical-perception-of-force-field-typing-rules monthly 0.5 2019-02-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1525889441361-H61W38UNEE7BSSYZYB3H/smarty-smirky.jpg Publications - Toward learned chemical perception of force field typing rules https://www.choderalab.org/publications/2018/7/20/overview-of-the-sampl6-host-guest-binding-affinity-prediction-challenge monthly 0.5 2019-02-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1532104811381-ZYB9WGD1MVGIGCUT46UC/CB8-G9.png Publications - Overview of the SAMPL6 host-guest binding affinity prediction challenge https://www.choderalab.org/publications/2016/7/11/an-open-library-of-human-kinase-domain-constructs-for-automated-bacterial-expression monthly 0.5 2019-07-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1507391736283-S9KD1AEFRV57WYIFQYI3/kinome-expression-tree.jpg Publications - An open library of human kinase domain constructs for automated bacterial expression https://www.choderalab.org/publications/2018/7/13/pka-measurements-for-the-sampl6-prediction-challenge-for-a-set-of-kinase-inhibitor-like-fragments monthly 0.5 2019-07-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1531494595904-8FOC3XP0M06HDBVDE2JX/pka-graphic.png Publications - pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments https://www.choderalab.org/publications/2018/6/29/acquired-resistance-to-idh-inhibition-through-trans-or-cis-dimer-interface-mutations monthly 0.5 2018-08-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1530282323117-0W0QA99C3M96ZRPCL6G5/IDH2.jpg Publications - Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations https://www.choderalab.org/publications/abl-resistance monthly 0.5 2019-07-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1514045366278-EGXXTWFVJ5HBO4MJ376B/kinase-mutations.jpg Publications - Predicting resistance of clinical Abl mutations to targeted kinase inhibitors using alchemical free-energy calculations https://www.choderalab.org/publications/2018/5/22/bayesian-analysis-of-isothermal-titration-calorimetry-for-binding-thermodynamics monthly 0.5 2019-03-03 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1526995930276-BA4OUCIA8BSENI8HW5SY/bayesian-itc.jpg Publications - Bayesian analysis of isothermal titration calorimetry for binding thermodynamics https://www.choderalab.org/publications/2018/2/16/quantifying-configuration-sampling-error-in-langevin-simulations-of-complex-molecular-systems monthly 0.5 2019-09-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1518823921150-JMVJZMN10FLM4298DOTS/quantifying-langevin-error.jpg Publications - Quantifying configuration-sampling error in Langevin simulations of complex molecular systems https://www.choderalab.org/publications/2018/3/25/open-force-field-consortium-escaping-atom-types-using-direct-chemical-perception-with-smirnoff-v01 monthly 0.5 2019-02-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1522018101963-QO2U1865TXDZ90JIRJ8S/smirnoff.png Publications - Escaping atom types in force fields using direct chemical perception https://www.choderalab.org/publications/2017/11/20/a-dynamic-mechanism-for-allosteric-activation-of-aurora-kinase-a-by-activation-loop-phosphorylation monthly 0.5 2018-05-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1511204091083-IJA05BBTT6F8MJ9HZ4ZX/AurA-graphic.png Publications - A dynamic mechanism for allosteric activation of Aurora kinase A by activation loop phosphorylation https://www.choderalab.org/publications/2018/2/5/quantitative-self-assembly-prediction-yields-targeted-nanomedicines monthly 0.5 2018-08-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1517879213640-SYYBYB02CSXOE271ZPJ3/nanoparticle.gif Publications - Quantitative self-assembly prediction yields targeted nanomedicines https://www.choderalab.org/publications/2017/11/29/biomolecular-simulations-under-realistic-macroscopic-salt-conditions monthly 0.5 2019-05-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1512007219131-A0SAF1PKGK8DPBEVFI48/saltswap-thumbnail.png Publications - Biomolecular simulations under realistic macroscopic salt conditions https://www.choderalab.org/publications/2017/9/20/binding-modes-of-ligands-using-enhanced-sampling-blues-rapid-decorrelation-of-ligand-binding-modes-using-nonequilibrium-candidate-monte-carlo monthly 0.5 2018-08-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1505900292716-AQZE4KXPJ109H0LS80W8/blues.png Publications - Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes Using Nonequilibrium Candidate Monte Carlo https://www.choderalab.org/publications/2016/12/17/openmm-7-rapid-development-of-high-performance-algorithms-for-molecular-dynamics monthly 0.5 2018-05-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482032349550-WFRL8IXI0SNGKMFWFI6M/image-asset.png Publications - OpenMM 7: Rapid Development of High Performance Algorithms for Molecular Dynamics https://www.choderalab.org/publications/2017/1/31/approaches-for-calculating-solvation-free-energies-and-enthalpies-demonstrated-with-an-update-of-the-freesolv-database monthly 0.5 2019-02-15 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1485909722123-L557SC6ZUU89Q5RT24SA/image-asset.png Publications - Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database https://www.choderalab.org/publications/2016/11/22/acidification-enhances-production-of-l-2-hydroxyglutarate-through-alternative-substrate-use-by-dehydrogenase-enzymes monthly 0.5 2018-08-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479846108971-MJ0IKUJSBY5PCURKJ27L/image-asset.png Publications - L-2-Hydroxyglutarate production arises from noncanonical enzyme function at acidic pH https://www.choderalab.org/publications/2016/11/25/a-conserved-water-mediated-hydrogen-bond-network-governs-allosteric-activation-in-aurora-kinase-a monthly 0.5 2018-08-14 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1480100447165-DW9SQA5OA0U0YAAVWEYN/image-asset.jpeg Publications - A water-mediated allosteric network governs activation of Aurora kinase A https://www.choderalab.org/publications/2016/8/3/mechanistically-distinct-cancer-associated-mtor-activation-clusters-predict-sensitivity-to-rapamycin monthly 0.5 2018-05-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1470258742572-8YSAFJUSORYT9RN3EDVM/image-asset.jpeg Publications - Mechanistically distinct cancer-associated mTOR activation clusters predict sensitivity to rapamycin https://www.choderalab.org/publications/2016/7/11/measuring-experimental-cyclohexane-water-distribution-coefficients-for-the-sampl5-challenge monthly 0.5 2018-05-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1468258782358-56K26SAQ282BNG66LW91/image-asset.jpeg Publications - Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge https://www.choderalab.org/publications/2015/5/19/l1wso8cubio6hq0wua9lcmggmdqdrw monthly 0.5 2017-11-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1432060396449-4I1JZBTBRIV6SAXOFT34/image-asset.png Publications - Ensembler: Enabling high-throughput molecular simulations at the superfamily scale https://www.choderalab.org/publications/2015/6/30/a-simple-method-for-automated-equilibration-detection-in-molecular-simulations monthly 0.5 2016-11-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1435665501398-UOMNQJ8MU7HO5OS99OQE/image-asset.jpeg Publications - A simple method for automated equilibration detection in molecular simulations https://www.choderalab.org/publications/2016/7/11/modeling-error-in-experimental-assays-using-the-bootstrap-principle-understanding-discrepancies-between-assays-using-different-dispensing-technologies monthly 0.5 2017-03-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1468258110473-I2MUMFI4FHFPG84FQQ1C/dispensing-errors-manuscript.jpg Publications - Modeling error in experimental assays using the bootstrap principle: Understanding discrepancies between assays using different dispensing technologies https://www.choderalab.org/publications/2015/8/1/avoiding-accuracy-limiting-pitfalls-in-the-study-of-protein-ligand-interactions-with-isothermal-titration-calorimetry monthly 0.5 2016-07-11 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1438476320589-D6DLZIJBDJP07P71IM0D/image-asset.png Publications - Avoiding accuracy-limiting pitfalls in the study of protein-ligand interactions with isothermal titration calorimetry https://www.choderalab.org/publications/2015/8/1/hypoxia-induces-production-of-l-2-hydroxyglutarate monthly 0.5 2016-11-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1438448169325-0Y612TJSTJ6MR1LD1KYC/image-asset.png Publications - Hypoxia induces production of L-2-hydroxyglutarate https://www.choderalab.org/publications/2015/6/2/towards-automated-benchmarking-of-atomistic-forcefields-neat-liquid-densities-and-static-dielectric-constants-from-the-thermoml-data-archive monthly 0.5 2016-07-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1433288123085-8G1JWKY7NVOIRTB3XTYR/image-asset.png Publications - Towards Automated Benchmarking of Atomistic Forcefields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive https://www.choderalab.org/publications/2014/4/26/markov-state-models-of-biomolecular-conformational-dynamics monthly 0.5 2015-06-10 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398563003239-P9KCT9JPETU2EU33JQ4D/image-asset.png Publications - Markov state models of biomolecular conformational dynamics https://www.choderalab.org/publications/2014/4/26/spectral-rate-theory-for-two-state-kinetics monthly 0.5 2014-06-16 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398560110250-B86SR4XKF5KKLENYWNVB/image-asset.png Publications - Spectral rate theory for two-state kinetics https://www.choderalab.org/publications/2014/4/26/time-step-rescaling-recovers-continuous-time-dynamical-properties-for-discrete-time-langevin-integration-of-nonequilibrium-systems monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398559185631-2XA5GKLR7X81QTUWTWPL/image-asset.png Publications - Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems https://www.choderalab.org/publications/2014/4/26/identifying-ligand-binding-sites-and-poses-using-gpu-accelerated-hamiltonian-replica-exchange-molecular-dynamics monthly 0.5 2015-07-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398555791367-LD6NBYM98HAP4PAVNI6Z/image-asset.jpeg Publications - Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics https://www.choderalab.org/publications/2014/4/26/systematic-improvement-of-a-classical-molecular-model-of-water monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398558772216-K9Y6UKELJFD9WE3IBYL7/image-asset.png Publications - Systematic improvement of a classical molecular model of water https://www.choderalab.org/publications/2014/4/26/entropy-enthalpy-compensation-role-and-ramifications-for-rational-ligand-design monthly 0.5 2015-07-18 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398556220953-6BPIFF9FXOXW0P1P4LPY/image-asset.png Publications - Entropy-enthalpy compensation: Role and ramifications for rational ligand design https://www.choderalab.org/publications/2014/4/26/using-nonequilibrium-fluctuation-theorems-to-understand-and-correct-errors-in-equilibrium-and-nonequilibrium-discrete-langevin-dynamics-simulations monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398558891830-H33NCY3CAYWP6QKQP45V/image-asset.png Publications - Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics simulations https://www.choderalab.org/publications/2014/4/26/openmm-4-a-reusable-extensible-hardware-independent-library-for-high-performance-molecular-simulation monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398561676519-81RZCYMG9HM185FMATEQ/image-asset.png Publications - OpenMM 4: A reusable, extensible, hardware independent library for high performance molecular simulation https://www.choderalab.org/publications/2014/4/26/the-limitations-of-constant-force-feedback-experiments monthly 0.5 2015-08-03 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398561886381-56A93BQPGYS3379MYOFC/image-asset.png Publications - The limitations of constant-force-feedback experiments https://www.choderalab.org/publications/2014/4/26/on-the-use-of-experimental-observations-to-bias-simulated-ensembles monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398564503152-RRRQS7O8EFJQS0LHTR2M/image-asset.png Publications - On the use of experimental observations to bias simulated ensembles https://www.choderalab.org/publications/2014/4/26/the-molten-globule-state-is-unusually-deformable-under-mechanical-force monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398562152975-P4SE73B3W4H75QW3B143/image-asset.png Publications - The molten globule state is unusually deformable under mechanical force https://www.choderalab.org/publications/2014/4/26/replica-exchange-and-expanded-ensemble-simulations-as-gibbs-sampling-simple-improvements-for-enhanced-mixing monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398559563668-6N98HT5WLF52XIZXONJZ/image-asset.png Publications - Replica exchange and expanded ensemble simulations as Gibbs sampling: Simple improvements for enhanced mixing https://www.choderalab.org/publications/2014/4/26/the-ribosome-modulates-nascent-protein-folding monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398562422237-YJB57ZSEQWRQRYL8GMFM/image-asset.png Publications - The ribosome modulates nascent protein folding https://www.choderalab.org/publications/2014/4/26/nonequilibrium-candidate-monte-carlo-is-an-efficient-tool-for-equilibrium-simulation monthly 0.5 2016-12-26 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398559688020-ATE7OA0SSIRDIEZQEB7I/image-asset.png Publications - Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation https://www.choderalab.org/publications/2014/4/26/splitting-probabilities-as-a-test-of-reaction-coordinate-choice-in-single-molecule-experiments monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398564355481-C6A0JSHU18Z3K5YD25V9/image-asset.png Publications - Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments https://www.choderalab.org/publications/2018/6/7/a-robust-approach-to-estimating-rates-from-time-correlation-functions monthly 0.5 2018-06-07 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1528403724313-O79T1GHMNL56NZ8CWU2V/robust-rates.jpg Publications - A robust approach to estimating rates from time-correlation functions https://www.choderalab.org/publications/2014/4/26/the-social-network-of-protein-conformations monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1436539552119-O9Y93BDC9SEX34UNQT8M/social-network.png Publications - The Social Network (of protein conformations) https://www.choderalab.org/publications/2016/7/11/bayesian-hidden-markov-model-analysis-of-single-molecule-force-spectroscopy-characterizing-kinetics-under-measurement-uncertainty monthly 0.5 2016-07-12 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1468285043542-Z8IQR8AXU8X2PCVEG85X/single-molecule-setup.png Publications - Bayesian hidden Markov model analysis of single-molecule force spectroscopy: Characterizing kinetics under measurement uncertainty https://www.choderalab.org/publications/2014/4/26/systematic-errors-in-isothermal-titration-calorimetry-concentrations-and-baselines monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398558646490-0R5L14W1JF99M1B3GKN9/image-asset.png Publications - Systematic errors in isothermal titration calorimetry: Concentrations and baselines https://www.choderalab.org/publications/2014/4/26/dynamical-reweighting-improved-estimates-for-dynamical-properties-from-simulations-at-multiple-temperatures monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398565329261-GA2GEHALRK40Z7FZ7PL5/image-asset.png Publications - Dynamical reweighting: Improved estimates for dynamical properties from simulations at multiple temperatures https://www.choderalab.org/publications/2014/4/26/optimal-use-of-data-in-parallel-tempering-simulations-for-the-construction-of-discrete-state-markov-models-of-biomolecular-dynamics monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398565125738-1W551K0MDUUW5VPA8R2S/image-asset.png Publications - Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics https://www.choderalab.org/publications/2014/4/26/markov-models-of-molecular-kinetics-generation-and-validation monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398565528070-FNOVL9299TZXZM8H651O/image-asset.png Publications - Markov models of molecular kinetics: Generation and validation https://www.choderalab.org/publications/2014/4/26/free-energy-methods-in-drug-discovery-and-design-progress-and-challenges monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398556472198-ZQ7HB280EJGLG4A1IA0B/image-asset.png Publications - Free energy methods in drug discovery and design: Progress and challenges https://www.choderalab.org/publications/2014/4/26/dynamical-fingerprints-a-theoretical-framework-for-understanding-biomolecular-processes-by-combination-of-simulation-and-kinetic-experiments monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398566156433-HD3MMVK68MW6VCZNO1QH/image-asset.png Publications - Dynamical fingerprints: A theoretical framework for understanding biomolecular processes by combination of simulation and kinetic experiments https://www.choderalab.org/publications/2014/4/26/estimating-equilibrium-ensemble-averages-using-multiple-time-slices-from-driven-nonequilibrium-processes monthly 0.5 2016-11-04 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398564720542-AXZVPSNE1UBNNWWFY0O9/image-asset.png Publications - Estimating equilibrium ensemble averages using multiple time slices from driven nonequilibrium processes https://www.choderalab.org/publications/2014/4/26/probability-distributions-of-molecular-observables-computed-from-markov-models-ii-uncertainties-in-observables-and-their-time-evolution monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398566402436-H4VV9MVZSNSIZV3RNW5R/observable-uncertainty.png Publications - Probability distributions of molecular observables computed from Markov models. II. Uncertainties in observables and their time-evolution https://www.choderalab.org/publications/2014/4/26/the-mechanical-properties-of-pcna-implications-for-the-loading-and-function-of-a-dna-sliding-clamp monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398566670001-RAP6J3ETECNEORKFRHPK/image-asset.jpeg Publications - The mechanical properties of PCNA: Implications for the loading and function of a DNA sliding clamp https://www.choderalab.org/publications/2014/4/26/current-status-of-the-amoeba-polarizable-force-field monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398559893681-FM2BKYZMRHQGHPSY789C/image-asset.png Publications - Current status of the AMOEBA polarizable force field https://www.choderalab.org/publications/2014/4/26/optimal-estimators-and-asymptotic-variances-for-nonequilibrium-path-ensemble-averages monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398564894277-6KCNZ0OQ2GQDDZS2WM5D/image-asset.png Publications - Optimal estimators and asymptotic variances for nonequilibrium path-ensemble averages https://www.choderalab.org/publications/2014/4/26/bayesian-comparison-of-markov-models-of-molecular-dynamics-with-detailed-balance-constraint monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398566877857-XSITM77TX2O36V6ZZREF/bayesian-comparison-markov-models.png Publications - Bayesian comparison of Markov models of molecular dynamics with detailed balance constraint https://www.choderalab.org/publications/2014/4/26/statistically-optimal-analysis-of-samples-from-multiple-equilibrium-states monthly 0.5 2015-07-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1437866304961-KQHX64QLJ5FUR9OVW7FY/image-asset.png Publications - Statistically optimal analysis of samples from multiple equilibrium states https://www.choderalab.org/publications/2015/5/27/technical-report-self-consistent-definition-and-computation-of-the-electrostatic-field-for-the-amber-and-related-forcefields-with-particle-mesh-ewald monthly 0.5 2015-05-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1432728876578-YN0ZDGJ4OH5GOI2H8UZP/image-asset.png Publications - Technical Report: Self-consistent definition and computation of the electrostatic field for the Amber and related forcefields with particle-mesh Ewald https://www.choderalab.org/publications/2014/4/26/predicting-small-molecule-solvation-free-energies-a-blind-challenge-test-for-computational-chemistry monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398556917501-IC84U0O0HRRRM450QGB1/image-asset.png Publications - Predicting small-molecule solvation free energies: A blind challenge test for computational chemistry https://www.choderalab.org/publications/2014/4/26/reating-entropy-and-conformational-changes-in-implicit-solvent-simulations-of-small-molecules monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398557137508-WBGFZZCC92WD2X15R5R4/entropy-solvation.png Publications - Treating entropy and conformational changes in implicit solvent simulations of small molecules https://www.choderalab.org/publications/2014/4/26/accurate-and-efficient-corrections-for-missing-dispersion-interactions-in-molecular-simulations monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398557429550-X4A6YFF5KJUSE80U8I1A/image-asset.png Publications - Accurate and efficient corrections for missing dispersion interactions in molecular simulations https://www.choderalab.org/publications/2014/4/26/alchemical-free-energy-calculations-ready-for-prime-time monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398557795483-OTJ88ZKLHHTVWSJM8KCP/binding-free-energy.png Publications - Alchemical free energy calculations: Ready for prime time? https://www.choderalab.org/publications/2014/4/26/predicting-absolute-ligand-binding-free-energies-to-a-simple-model-site monthly 0.5 2016-11-13 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398557951810-C6QUWHORQQCM9QT4LGB7/image-asset.png Publications - Predicting absolute ligand binding free energies to a simple model site. https://www.choderalab.org/publications/2014/4/26/the-protein-folding-problem-when-will-it-be-solved monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398567296910-QKO4CY2KPF5TZA4XFRJP/image-asset.png Publications - The protein folding problem: When will it be solved? https://www.choderalab.org/publications/2014/4/26/confine-and-release-method-obtaining-correct-binding-free-energies-in-the-presence-of-protein-conformational-change monthly 0.5 2016-11-13 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398558128256-78Y4Y3QNYV47H8Z6MZMP/image-asset.png Publications - Confine-and-release method: Obtaining correct binding free energies in the presence of protein conformational change https://www.choderalab.org/publications/2014/4/26/protein-folding-by-zipping-and-assembly monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398567137753-L5IIXGW9M9B33NSB2LL5/image-asset.jpeg Publications - Protein Folding by Zipping and Assembly https://www.choderalab.org/publications/2014/4/26/automatic-discovery-of-metastable-states-for-the-construction-of-markov-models-of-macromolecular-conformational-dynamics monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398567027249-02SSPKQF9TCEB93KHHK1/image-asset.jpeg Publications - Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics https://www.choderalab.org/publications/2014/4/26/comparison-of-charge-models-for-fixed-charge-force-fields-small-molecule-hydration-free-energies-in-explicit-solvent monthly 0.5 2016-11-13 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398557582957-RMDOK9J6GXINA3D78G0T/image-asset.png Publications - Comparison of charge models for fixed-charge force fields: Small-molecule hydration free energies in explicit solvent https://www.choderalab.org/publications/2014/4/26/long-time-protein-folding-dynamics-from-short-time-molecular-dynamics-simulations monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398567444258-B3SZWOVWBJ42NU8N5KIV/image-asset.png Publications - Long-time protein folding dynamics from short-time molecular dynamics simulations https://www.choderalab.org/publications/2014/3/1/use-of-the-weighted-histogram-analysis-method-for-the-analysis-of-simulated-and-parallel-tempering-simulations monthly 0.5 2015-07-22 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1393730317255-HJ3ZNOKWPRAYK055O4T6/alanine-dipeptide-2dpmf.jpg Publications - Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations https://www.choderalab.org/publications/2014/4/26/on-the-use-of-orientational-restraints-and-symmetry-corrections-in-alchemical-free-energy-calculations monthly 0.5 2016-11-13 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1398558242406-LO3ZN9OJ2F6KBT7WDZEQ/image-asset.png Publications - On the use of orientational restraints and symmetry corrections in alchemical free energy calculations https://www.choderalab.org/publications/2014/2/25/moped-method-for-optimizing-physical-energy-parameters-using-decoys monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1393476477522-VFLMY9VYS5NU99IWTT66/image-asset.jpeg Publications - MOPED: Method for optimizing physical energy parameters using decoys https://www.choderalab.org/publications/2014/2/23/an-alternative-explanation-for-the-catalytic-proficiency-of-orotidine-5-phosphate-decarboxylase monthly 0.5 2016-04-06 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1393476530887-2YQHZ9CYHV5H2VMBID8U/moped.jpg Publications - An alternative explanation for the catalytic proficiency of orotidine 5'-phosphate decarboxylase https://www.choderalab.org/publications/category/technical+report monthly 0.5 https://www.choderalab.org/publications/category/review monthly 0.5 https://www.choderalab.org/publications/category/preprint monthly 0.5 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https://www.choderalab.org/publications/tag/Alpha+Lee monthly 0.5 https://www.choderalab.org/compstatsclub daily 0.75 2017-06-23 https://www.choderalab.org/compstatsclub/2017/6/23/23-june-2017-chaya-stern-prior-distribution-for-variance-parameters-in-hierarchical-models monthly 0.5 2017-06-23 https://www.choderalab.org/compstatsclub/2017/6/15/16-june-2017-andrea-rizzi-a-common-derivation-for-markov-chain-monte-carlo-algorithms-with-tractable-and-intractable-targets monthly 0.5 2017-06-15 https://www.choderalab.org/compstatsclub/2017/6/9/9-june-2017-patrick-grinaway-likelihood-free-inference-via-classification monthly 0.5 2017-06-09 https://www.choderalab.org/compstatsclub/2017/5/23/2-june-2017-bas-rustenburg-discussing-sequential-monte-carlo-sampling-for-dsge-models monthly 0.5 2017-05-25 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1495566216254-55R5NDLEBXTV0AQQXDZQ/image-asset.png Computational Statistics Club - 2 June 2017 - Bas Rustenburg - discussing "Sequential Monte Carlo Sampling for DSGE models" - Summary Summary We develop a sequential Monte Carlo (SMC) algorithm for estimating Bayesian dynamic stochastic general equilibrium (DSGE) models; wherein a particle approximation to the posterior is built iteratively through tempering the likelihood. Using two empirical illustrations consisting of the Smets and Wouters model and a larger news shock model we show that the SMC algorithm is better suited for multimodal and irregular posterior distributions than the widely used random walk Metropolis–Hastings algorithm. We find that a more diffuse prior for the Smets and Wouters model improves its marginal data density and that a slight modification of the prior for the news shock model leads to drastic changes in the posterior inference about the importance of news shocks for fluctuations in hours worked. Unlike standard Markov chain Monte Carlo (MCMC) techniques; the SMC algorithm is well suited for parallel computing. Copyright © 2014 John Wiley & Sons, Ltd https://www.choderalab.org/compstatsclub/2017/5/25/25-may-2017-jason-wagoner-some-tricks-to-reduce-correlation-times-in-ghmc-simulations monthly 0.5 2017-05-25 https://www.choderalab.org/compstatsclub/2017/5/19/19-may-2017- monthly 0.5 2017-05-19 https://www.choderalab.org/compstatsclub/2017/5/19/6d8b6e8p1048a7mxh380n7gqnv1sff monthly 0.5 2017-05-19 https://www.choderalab.org/compstatsclub/2017/5/19/28-apr-2017-rajesh-ranganath-implicit-models-and-posterior-approximations monthly 0.5 2017-05-19 https://www.choderalab.org/compstatsclub/2017/5/19/7-apr-2017-josh-fass-distill-article-on-momentum monthly 0.5 2017-05-19 https://www.choderalab.org/compstatsclub/2017/5/19/31-mar-2017-patrick-grinaway-parallel-resampling-in-the-particle-filter monthly 0.5 2017-05-19 https://www.choderalab.org/compstatsclub/2017/2/6/10th-feb-efficient-sequential-monte-carlo-with-multiple-proposals-and-control-variables monthly 0.5 2017-02-07 https://www.choderalab.org/compstatsclub/2017/2/1/3-feb-2017-deep-unsupervised-learning-using-nonequilibrium-thermodynamics monthly 0.5 2017-02-01 https://www.choderalab.org/compstatsclub/2016/11/28/schedule-for-december-2016 monthly 0.5 2016-11-28 https://www.choderalab.org/compstatsclub/2016/11/11/schedule-for-november-2016 monthly 0.5 2016-11-25 https://www.choderalab.org/compstatsclub/2016/8/15/schedule-for-september-2016 monthly 0.5 2016-10-04 https://www.choderalab.org/compstatsclub/2016/8/1/schedule-for-august-2016 monthly 0.5 2016-08-15 https://www.choderalab.org/compstatsclub/2016/5/19/updated-schedule monthly 0.5 2016-08-01 https://www.choderalab.org/compstatsclub/2016/5/19/specific-themes-of-interest monthly 0.5 2016-05-19 https://www.choderalab.org/compstatsclub/tag/CSC monthly 0.5 https://www.choderalab.org/compstatsclub/tag/MCMC monthly 0.5 https://www.choderalab.org/compstatsclub/tag/kernel+methods monthly 0.5 https://www.choderalab.org/compstatsclub/tag/goodness+of+fit monthly 0.5 https://www.choderalab.org/compstatsclub/tag/computational+statistics+club monthly 0.5 https://www.choderalab.org/research-projects daily 0.75 2020-05-30 https://www.choderalab.org/research-projects/rational-design-of-small-molecules monthly 0.5 2017-07-01 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479072992806-YVI1G48NULOO7LK2S6HF/image-asset.gif Research Projects - Rational design of small molecules alchemical free energy calculation of abl:imatinib https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479000359821-RKCOP3RYEP96P7T5H842/image-asset.jpeg Research Projects - Rational design of small molecules https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479002418794-KDAYG1J4OK6HNMUFWCD5/merck_m_detail.png Research Projects - Rational design of small molecules Merck Kgga https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479002704826-GWH23YN76XGPCRL7HKQQ/image-asset.png Research Projects - Rational design of small molecules Astrazeneca https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479002549366-HLT9JQ78IOOQNQ7GTELV/image-asset.png Research Projects - Rational design of small molecules Gerstner Young investigator award https://www.choderalab.org/research-projects/kinase-inhibitor-selectivity monthly 0.5 2020-05-30 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479005106137-FVDVUBEOATE2BKZ4B6UH/kinase-inhibitor-selectivity.jpg Research Projects - Kinase inhibitor selectivity and design From Nature Biotech. 23:329, 2005. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479005688745-GZANTQPREVB0ZWPMZ4VH/image-asset.jpeg Research Projects - Kinase inhibitor selectivity and design https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479005999982-AHC18DZS356WQLBGMPE8/image-asset.jpeg Research Projects - Kinase inhibitor selectivity and design https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1506087076817-OXGYMMEK4VQWWYU5VVH1/nih-logo.jpg Research Projects - Kinase inhibitor selectivity and design NIGMS 1 R01 GM121505 01 https://www.choderalab.org/research-projects/predicting-drug-susceptibility-and-the-emergence-of-drug-resistance monthly 0.5 2020-05-30 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479092602222-J6UFWP6MMQQ53EAHM3WA/image-asset.jpeg Research Projects - Predicting drug susceptibility and the emergence of drug resistance Many mutations in Abl are located in the kinase domain, the molecular target of therapy (figure from cbioportal). https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479093013309-B33YPWF2NLKVK3AURDKE/image-asset.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479092704653-HJEGNOTU61K9EYRSFLW9/abl-mutations-2HYY-cbioportal.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance Abl residues observed mutated in tumors (superimposed on pdb:2HYY) https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479096373144-IKNQ93IAYUFA9C31URLJ/mtor-analysis-diagram.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance Assessing the impact of CLINICALLY-OBSERVED MUTATIONS of mtor using folding@home https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479096528814-5EN3IWXAQA2W6RPGAMPW/white_mtor_mutants.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance Clinically-identified mutants in the kinase and fat domains of mtor https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479096498026-2KPVW7RRSG77K3G8RRKY/jci_paper_fig.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance folding@home simulations reveal loss of key contacts in the mtor kinase domain due to s2215f mutation https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1590810614417-INC39BE9DOZ07SZTUCR9/long-tail-of-mutations.jpg Research Projects - Predicting drug susceptibility and the emergence of drug resistance Over 87% of missense mutations in kinases have been observed less than ten times in the MSK-IMPACT dataset, and therefore have not been characterized clinically, biochemically, or biophysically. https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479099538510-5EIJZCU12G1LTVJR633V/abl-dasatinib-resistance.jpg Research Projects - Predicting drug susceptibility and the emergence of drug resistance abl mutation dynamics in response to dasatinib treatment. (Leukemia 26:172, 2012) https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479093963519-N43PBSFXJ075SQPVERYX/image-asset.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance LOUIS V GERSTNER YOUNG INVESTIGATOR AWARD https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479093928408-5YTOJHJJYAYUEYDGABY8/image-asset.png Research Projects - Predicting drug susceptibility and the emergence of drug resistance MSKCC FUNCTIONAL GENOMICS INITIATIVE FUNDED BY CYCLE FOR SURVIVAL https://www.choderalab.org/research-projects/2016/11/12/targeting-protein-methyltransferases monthly 0.5 2016-11-17 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479002230419-WHBPUE7OMP1RMIWDHT20/image-asset.png Research Projects - Epigenetic cancer targets Protein methyltransferase NSD1 (pdbid 4h12) https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479097563970-EIP8JVPP1AAQ3OMYZIWH/starr-cancer-consortium.png Research Projects - Epigenetic cancer targets STARR CANCER CONSORTIUM https://www.choderalab.org/research-projects/targeted-nanoparticles monthly 0.5 2020-05-30 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479099228253-N8KUD2GU3VVAP9KOWKOI/image-asset.gif Research Projects - Nanoparticles for targeted drug delivery https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479089584235-YF58Z1PM6XP4E7HFINAJ/F12_v2.jpg Research Projects - Nanoparticles for targeted drug delivery https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1590803186426-7VM6RKUPYYI35V4KQTN7/552px-Critical_radius1.svg.png Research Projects - Nanoparticles for targeted drug delivery illustration of critical nucleus size in nucleation theory. Image from mmarso https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1590807858887-0IER3WYE64JDLY8CQ3PH/gimlet.jpg Research Projects - Nanoparticles for targeted drug delivery https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1590802331951-MTRCXQ71VYHQWPUHKAPX/indocyanine%2Bdyes.jpg Research Projects - Nanoparticles for targeted drug delivery examples of indocyanine dyes that efficiently form nanoparticles https://www.choderalab.org/research-projects/automated-ligand-design monthly 0.5 2017-06-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479016583415-QKVFSER35DEJMYFJ4S8T/image-asset.gif Research Projects - Automated ligand design imatinib to nilotinib geometry proposal in abl https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479016446542-0YDUHOCBLW9GSS8USPZP/image-asset.gif Research Projects - Automated ligand design erlotinib to nilotinib geometry proposals in solvent https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479091366265-N2XB0RJNUUXDFNQ3XOXI/image-asset.jpeg Research Projects - Automated ligand design imatinib to ponatinib common scaffold (blue) and newly built atoms (red) https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1498580690165-8KVB14FHU2G5DSI6SBJ4/image-asset.png Research Projects - Automated ligand design SILICON THERAPEUTICS https://www.choderalab.org/research-projects/model-systems monthly 0.5 2022-09-20 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479008204387-2WHZZPBYZAFQVQ153W20/image-asset.jpeg Research Projects - Automated biophysical measurements to drive improvements in physical modeling accuracy https://www.choderalab.org/research-projects/rational-design-of-allosteric-modulators monthly 0.5 2016-12-26 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1479008858143-0GGJX5RP80L9KKG8GIG8/image-asset.png Research Projects - Design of small molecule allosteric modulators H-RAS GTPASE [5P21] WITH GTP ANALOG. https://www.choderalab.org/research-projects/2016/12/26/bayesian-inference-and-error-modeling-for-experimental-data monthly 0.5 2016-12-27 https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482785694540-096JE9LGLN3J54OZNNOP/image-asset.jpeg Research Projects - Bayesian inference and error modeling for experimental data https://images.squarespace-cdn.com/content/v1/530562f9e4b06fd3c041e221/1482785408654-R8C37W35BVU8HPJE864H/image-asset.jpeg Research Projects - Bayesian inference and error modeling for experimental data Bootstrap modeling of a simple dilution series generated using disposable tips, washable tips, and acoustic dispensing demonstrates how strikingly different bias and variance profiles emerge. Hanson et al. 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