@choderalab

Chodera lab // Memorial Sloan Kettering Cancer Center

Pinned repositories

  1. pymbar

    Python implementation of the multistate Bennett acceptance ratio (MBAR)

    Python 55 34

  2. ensembler

    Automated omics-scale protein modeling and simulation setup.

    Python 28 13

  3. yank

    An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

    Python 40 30

  4. assaytools

    Modeling and Bayesian analysis of fluorescence and absorbance assays.

    Python 8 8

  5. software-development

    A primer on software development best practices for computational chemistry

    65 18

  6. openmmtools

    An OpenMM toolkit with test systems, integrators, and alchemical support

    Python 40 18

  • Open source toolkit for predicting bacterial porin permeation

    Python 1 MIT Updated Oct 19, 2018
  • Bacterial porin permeation calculation examples for iapetus

    Python 1 MIT Updated Oct 19, 2018
  • Experiments with expanded ensembles to explore chemical space

    Python 16 7 MIT 3 issues need help Updated Oct 19, 2018
  • An OpenMM toolkit with test systems, integrators, and alchemical support

    Python 40 18 MIT Updated Oct 19, 2018
  • Utilities to run on MPI.

    Python 1 MIT Updated Oct 18, 2018
  • Modeling and Bayesian analysis of fluorescence and absorbance assays.

    Python 8 8 LGPL-2.1 1 issue needs help Updated Oct 17, 2018
  • Records of ITC Experiments

    Jupyter Notebook Updated Oct 17, 2018
  • Code and data for the paper 'What makes a kinase promiscuous for inhibitors?'.

    Jupyter Notebook Updated Oct 16, 2018
  • PlasmidLibraryTools

    Jupyter Notebook 2 Updated Oct 15, 2018
  • Evaluating MSM-estimated mean first passage times

    Jupyter Notebook 1 MIT Updated Oct 11, 2018
  • An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

    Python 40 30 MIT Updated Oct 5, 2018
  • OpenMM testbed for constant-pH methodologies.

    Python 14 10 Updated Oct 5, 2018
  • SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)

    Jupyter Notebook MIT Updated Oct 4, 2018
  • A collection of protocols, primarily for automated protein expression and mutagenesis

    Python 2 3 Updated Oct 4, 2018
  • Titrato (name pending) is a set of tools for analyzing pKa data.

    Python MIT Updated Oct 3, 2018
  • Repository for SAMPL6 pKa measurements manuscript.

    Jupyter Notebook Updated Oct 1, 2018
  • Examples for MHC-peptide free energy calculations using YANK

    Python MIT Updated Sep 21, 2018
  • Reference pKa calculations for the SAMPL6 pKa challenge

    Jupyter Notebook Updated Sep 19, 2018
  • Examples for fragmenter

    Python MIT Updated Sep 18, 2018
  • Molecular simulation algorithms and computational statistics blog

    CSS 4 Updated Sep 17, 2018
  • Tools for setting up ITC experiments in an automated fashion using the Tecan EVO and Auto-iTC 200.

    Python 1 5 Updated Sep 17, 2018
  • Validation input files for YANK

    Jupyter Notebook 1 MIT Updated Sep 12, 2018
  • Standard experimental accuracy benchmark set for YANK.

    Jupyter Notebook 2 Updated Sep 11, 2018
  • Host-guest system data and simulations

    Python 2 Updated Sep 11, 2018
  • CHARMM and AMBER forcefields for OpenMM

    Python 8 8 Updated Sep 11, 2018
  • Examples for use of YANK - getyank.org

    Python 3 2 MIT Updated Sep 8, 2018
  • Jupyter Notebook Updated Sep 7, 2018
  • Ligandr code

    Python 3 LGPL-3.0 Updated Sep 7, 2018
  • Latex manuscript for the SAMPL6 epik and jaguar pKa paper

    TeX Updated Sep 5, 2018
  • A primer on software development best practices for computational chemistry

    65 18 Updated Aug 20, 2018