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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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January 03, 2019

What makes a kinase promiscuous for inhibitors?

January 03, 2019/ John Chodera
kinase-promiscuity.jpg

Hanson SM*, Georghiou G*, Miller WT, Rest JS, Chodera JD, Seeliger MA. 
Cell Chemical Biology 26:390, 2019. [DOI] [PDF] [GitHub]

A class of kinases are particularly promiscuous binders of small molecule inhibitors. Using combined biomolecular simulations and biochemical studies, we show that the promiscuity of DDR1, one of the major members of this class, is likely due to an unusually stable DFG-out conformation.  

January 03, 2019/ John Chodera/ Comment
article
submitted, paper, DDR1, Sonya Hanson, Markov state model, NIH grant R01 GM121505, NIH grant P30 CA008748, Cycle for Survival

John Chodera

  • The dynamic conformational ...
  • OpenPathSampling: A Python ...

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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