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src-imatinib-1040.jpg

Chodera lab // MSKCC

Changing drug discovery one ratio of partition functions at a time

Publications

John Chodera publications

Chodera lab // MSKCC

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ARTICLE TYPES

  • technical report (1)
  • commentary (2)
  • review (5)
  • preprint (51)
  • article (66)

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June 29, 2018

Acquired resistance to IDH inhibition through trans or cis dimer-interface mutations

June 29, 2018/ John Chodera
IDH2.jpg

Andrew M. Intlekofer,  Alan H. Shih,  Bo Wang,  Abbas Nazir,  Ariën S. Rustenburg,  Steven K. Albanese, Minal Patel, Christopher Famulare, Fabian M. Correa, Naofumi Takemoto, Vidushi Durani, Hui Liu, Justin Taylor, Noushin Farnoud, Elli Papaemmanuil, Justin R. Cross, Martin S. Tallman, Maria E. Arcila, Mikhail Roshal, Gregory A. Petsko, Bin Wu, Sung Choe, Zenon D. Konteatis, Scott A. Biller, John D. Chodera, Craig B. Thompson, Ross L. Levine, and Eytan M. Stein
Nature 559:125, 2018. [DOI] [PDF]

We probe the biochemical and biophysical mechanisms underlying an unusual set of clinical resistance mutations that appeared in trans in the IDH2 dimer interface in cancer patients treated with IDH2 inhibitors.

June 29, 2018/ John Chodera/ Comment
article
Bas Rustenburg, Steven Albanese, Craig Thompson, Andy Intlekofer, Ross Levine, Eytan Stein, Gregory Petsko, IDH2, nature

John Chodera

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  • alchemical free energy calculations
  • alchemical methods
  • Alpha Lee
  • Andrea Rizzi
  • Andrea Volkamer
  • arXiv
  • Bas Rustenburg
  • Bayesian inference
  • binding affinity
  • biomolecular dynamics
  • biophysical methods
  • bioRxiv
  • cancer
  • Chaya Stern
  • Christopher Bayly
  • COVID Moonshot
  • COVID-19
  • Cycle for Survival
  • Daniel Smith
  • David Mobley
  • eLife
  • experimental
  • Folding@home
  • force fields
  • forcefield parameterization
  • forcefield validation
  • Frank Noé
  • Frank von Delft
  • free energy calculations
  • GPU
  • Gregory Ross
  • Hannah Bruce Macdonald
  • ITC
  • Ivy Zhang
  • Iván Pulido
  • JCAMD
  • JCIM
  • JCTC
  • Jiaye Guo
  • John Chodera
  • Josh Fass
  • Ken Takaba
  • kinase
  • kinases
  • KinoML
  • Laura Rosen
  • Lee-Ping Wang
  • machine learning
  • machine learning potentials
  • Marcus Wieder
  • Markus Seeliger
  • Mehtap Isik
  • Michael Gilson
  • Michael Shirts
  • ML/MM
  • molecular dynamics
  • molecular simulation
  • MSM
  • mutations
  • NIH grant P30 CA008748
  • NIH grant R01 GM121505
  • NIH grant R01 GM124270
  • NIH grant R01 GM132386
  • NIH P30 CA008748
  • NIH R01 GM121505
  • NIH R01 GM132386
  • nonequilibrium statistical mechanics
  • NSF grant CHE 1738979
  • Open Force Field
  • Open Force Field Consortium
  • Open Force Field Initiative
  • OpenEye Toolkit
  • openforcefield
  • OpenMM
  • openpathsampling
  • optical traps
  • Peter Eastman
  • pKa
  • polarizable forcefields
  • preprint
  • protein folding
  • quantum chemistry
  • quantum machine learning
  • Rafal Wiewiora
  • rational drug design
  • SAMPL
  • SAMPL6
  • SARS-CoV-2
  • Simon Boothroyd
  • single-molecule experiments
  • SPICE dataset
  • statistical inference
  • Stefan Knapp
  • Steven Albanese
  • Sukrit Singh
  • targeted kinase inhibitors
  • tautomer ratios
  • Vijay Pande
  • William Glass
  • Yuanqing Wang