Congratulations to Tri-Institutional PhD Program in Chemical Biology (TPCB) graduate student and NSF GRFP recipient Chaya Stern on receiving a 2018 MolSSI Phase I Fellowship to support her work in developing new algorithms and open source software for Bayesian inference of force field parameters from experimental and quantum chemical data! You can learn more about Chaya's work in this area by listening to her PyData NYC 2017 talk or reading her MolSSI Fellowship Proposal, and hear more about what Chaya is up to by following her twitter feed.
The Open Forcefield Consortium [http://openforcefield.org] seeks a Lead Software Scientist to coordinate open source software development efforts for an interdisciplinary academic team developing next-generation molecular mechanics forcefields and associated parameterization infrastructure.
See the full job ad here.
We're excited to announce that Postdoctoral Fellow Dr. Gregory Ross has joined Schrödinger as a Senior Scientist, where he will be working to bring his expertise in statistical mechanics and semigrand canonical methods to their suite of molecular modeling and simulation tools.
You can see more fantastic work from Dr. Ross at his Google Scholar page, and check out his recent preprint on semigrand canonical methods for simulating realistic biomolecular salt concentrations on bioRxiv.
The Chodera lab was awarded an NIH R01 research grant to study the role of conformational reorganization energy in selective kinase inhibition. Because even evolutionarily related kinase can have vastly different energetic costs to adopt inhibitor-bound conformations, these difference can be exploited to design new selective inhibitors, but only with computational approaches to elucidate hidden conformational states and their energetic penalties.
You can read more about our research on selective kinase inhibitor design, or download the entire NIH R01 proposal we submitted here.
The Chodera lab has been awarded an NSF grant funding Data-Driven Discovery Science in Chemistry (D3SC) for a collaborative project with the laboratory of Michael Shirts (University of Colorado) that explores the use of advanced Bayesian methodologies for parameterization in molecular mechanics forcefields of small molecular liquids.
Congratulations to TPCB graduate student Chaya Stern for receiving a Diversity Scholarship to attend SciPy 2017 in Austin, TX July 10-16. SciPy is a conference focusing on scientific computing with Python, and brings together a community of open source software developers and users from industry, academia, and government to show off their projects, learn from each other, and collaborate to develop better code.
We're grateful to JumpTrading and NumFocus for providing the funds for this fellowship.
Christmas comes early! We've released a beta of OpenMM 7.1, packed with speed improvements and new features, including:
- Optimized clang builds of both Anaconda packages and ZIP installers, offering anywhere from a 30% to 50x boost for some applications that use the CPU platform.
- Custom Forces can now compute energy derivatives with respect to global parameters! Lambda dynamics can now be implemented via a CustomIntegrator.
- Gay-Berne ellipsoid potential!
- Bonded forces can now use periodic boundary conditions.
To get the updated OpenMM conda package, use the beta channel:
conda install -c omnia/label/beta openmm==7.1.0
If you have already been using the dev channel 7.1.0 nightly builds, force a downgrade first:
# Force downgrade to 7.0.1 conda install --yes -c omnia openmm==7.0.1 # Clear local cache conda clean -plti --yes # Install the beta conda install --yes -c omnia/label/beta openmm==7.1.0
Nightly dev builds are now called 7.2.0. You can always get the latest version with:
conda install --yes -c omnia/label/dev openmm
The NIH recently issued a request for information (RFI) on the role of preprints in NIH applications. You can read my response here. Many others shared insightful responses publicly, and ASAPbio has indexed them here.
Our lab is a core member of the Folding@home Consortium, a research network of 11 laboratories around the world that use Folding@home to study the molecular mechanisms underlying cancer and other diseases and identify new routes toward therapies. Together, we are aiming to recruit one million volunteers donating compute cycles to help us!
Please join us, especially if you have a GPU: Folding@home can harness the power of your GPU.
It costs nothing (other than your electrical bill) and provides a way to donate your idle computer cycles to biomedical research.
Other useful links:
- Learn about the Folding@home "One in a Million" campaign
- Read about how we use Folding@home to study molecular mechanisms of cancer
- See how far we've come according to current Folding@home statistics
- Learn more about the project via the Folding@home main page
- Read the over 130 scientific papers that have come from the Folding@home project
We are beyond thrilled to congratulate Chodera lab postdoc Sonya Hanson for being accepted into the inaugural Scientific Communication Summer Bootcamp at the Alan Alda Center for Communicating Science! The Center, founded by the veteran director/actor/writer Alan Alda (M*A*S*H, The West Wing, QED, and PBS' Scientific American Frontiers), strives to enhance public understanding of science by working with young scientists and health professionals to develop effective skills for disseminating and communicating science.
The Bootcamp is an intensive week-long program designed to aid scientists in honing their ability to communicate clearly with the public in a multitude of forums, training that is essential for supporting a healthy scientific enterprise in the United State, but which is far too often overlooked in science training programs. For those interested in what an intensive training program in science communication can look like, the Alda Center has posted the full Bootcamp program agenda online.
Sonya has been engaged in scientific communication and outreach activities throughout her career. She is a former editor of the Oxbridge Biotech Roundtable, maintains an active twitter feed and science blog covering a newsworthy science-related topics, blogs about her research into anticancer therapeutics on the Folding@home blog, was recently a featured guest blogger for the Biophysical Society, and a champion of open source salads.
Stay tuned for more from Sonya on her experiences at the Science Communication Summer Bootcamp.