@choderalab

Chodera lab // Memorial Sloan Kettering Cancer Center

Pinned repositories

  1. pymbar

    Python implementation of the multistate Bennett acceptance ratio (MBAR)

    Python 55 33

  2. ensembler

    Automated omics-scale protein modeling and simulation setup.

    Python 27 12

  3. yank

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

    Python 37 28

  4. assaytools

    Modeling and Bayesian analysis of fluorescence and absorbance assays.

    Python 8 7

  5. software-development

    A primer on software development best practices for computational chemistry

    59 16

  6. openmmtools

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

    Python 33 17

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

    Python 33 17 MIT Updated Jul 21, 2018
  • Investigating the error introduced by neglecting shadow work

    Python MIT Updated Jul 20, 2018
  • Python-centric Cookiecutter for Molecular Computational Chemistry Packages

    Python 31 8 MIT Updated Jul 20, 2018
  • Attempted implementation of Frank Noe's summer students's work on observable tICA

    Jupyter Notebook 2 Updated Jul 19, 2018
  • A collection of protocols, primarily for automated protein expression and mutagenesis

    Python 2 3 Updated Jul 19, 2018
  • An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

    Python 37 28 MIT Updated Jul 18, 2018
  • Selection of kinase constructs suitable for E coli expression

    HTML 3 Updated Jul 17, 2018
  • Jupyter Notebook Updated Jul 17, 2018
  • Experiments with expanded ensembles to explore chemical space

    Python 14 6 MIT 3 issues need help Updated Jul 14, 2018
  • Repository for SAMPL6 pKa measurements manuscript.

    Jupyter Notebook Updated Jul 13, 2018
  • Examples for use of YANK - getyank.org

    Python 3 2 MIT Updated Jul 6, 2018
  • Evaluating MSM-estimated mean first passage times

    Jupyter Notebook 1 MIT Updated Jul 3, 2018
  • Ligandr code

    Python 3 LGPL-3.0 Updated Jul 3, 2018
  • A primer on software development best practices for computational chemistry

    59 16 Updated Jul 2, 2018
  • Investigation into the effect of shadow work on nonequilibrium switching based relative free energy calculations

    Python MIT Updated Jun 28, 2018
  • Tools for Munging Folding@Home datasets

    Python 2 6 MIT Updated Jun 25, 2018
  • OpenMM testbed for constant-pH methodologies.

    Python 13 10 Updated Jun 21, 2018
  • Examples for fragmenter

    Python MIT Updated Jun 21, 2018
  • Experiments in adaptive sampling with trpzip2 [1] as a model system

    Python MIT Updated Jun 19, 2018
  • Standard experimental accuracy benchmark set for YANK.

    Jupyter Notebook 1 Updated Jun 8, 2018
  • Reference pKa calculations for the SAMPL6 pKa challenge

    Jupyter Notebook 1 Updated Jun 5, 2018
  • a collection of scripts and files to help in PDB retrieval for various projects

    Python 2 2 1 issue needs help Updated Jun 5, 2018
  • Titrato (name pending) is a set of tools for analyzing pKa data.

    Python MIT Updated Jun 6, 2018
  • Latex manuscript for the SAMPL6 epik and jaguar pKa paper

    TeX Updated Jun 5, 2018
  • Open source toolkit for predicting bacterial porin permeation

    Python MIT Updated May 29, 2018
  • Bacterial porin permeation calculation examples for iapetus

    Python MIT Updated May 28, 2018
  • Jupyter Notebook Updated May 25, 2018
  • Change Point detection

    Python 9 7 GPL-3.0 Updated May 24, 2018
  • SAMPL6 physicochemical property prediction challenge (logD, pKa and solubility)

    Jupyter Notebook MIT Updated May 2, 2018
  • Cheminformatic analysis of small molecule type drugs in DrugBank for their ability to form nanoparticles with indocyanine dyes.

    Jupyter Notebook 1 1 MIT Updated Apr 30, 2018