jchodera
Assistant Professor at the Memorial Sloan Kettering Cancer Center. Computational drug discovery, biophysics, and scalable Bayesian inference.
Memorial Sloan Kettering Cancer CenterNew York, NY
Pinned Repositories
openmmtools
A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.
pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
software-development
A primer on software development best practices for computational chemistry
yank
An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
jacs-dataset-analysis
Re-analysis of the Schrödinger JACS dataset
latex-cv
Example showing how LaTeX can be used to produce a nice-looking curriculum vitae (CV).
latex-manuscript-template
Simple LaTeX manuscript template
statmech-for-biochemists
A primer on statistical mechanics for biochemists
yank
GPU-accelerated calculation of ligand binding affinities in implicit and explicit solvent using alchemical free energy methodologies
openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
jchodera's Repositories
jchodera/statmech-for-biochemists
A primer on statistical mechanics for biochemists
jchodera/latex-cv
Example showing how LaTeX can be used to produce a nice-looking curriculum vitae (CV).
jchodera/jacs-dataset-analysis
Re-analysis of the Schrödinger JACS dataset
jchodera/openmm
OpenMM is a toolkit for molecular simulation using high performance GPU code.
jchodera/simple-simulate-complex
Simple protein-ligand complex simulation with OpenMM
jchodera/alchemical-best-practices
Best practice document for alchemical free energy calculations going to livecoms journal
jchodera/ambertools-feedstock
A conda-smithy repository for ambertools.
jchodera/benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
jchodera/Chem456
Web site for Chem 456 - Computational Biochemistry and Drug Design
jchodera/clusterutils-feedstock
A conda-smithy repository for clusterutils.
jchodera/conda-forge-pinning-feedstock
A conda-smithy repository for conda-forge-pinning.
jchodera/covid
MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store
jchodera/experiments-binding-affinity
jchodera/fah_prep
suite of functions to prepare simulations (docking, free energy) for use with folding at home.
jchodera/fragmenter-manuscript
jchodera/freeenergyframework
Package for consistent reporting of relative free energy results
jchodera/jdcthesis
John Chodera's PhD thesis latex source
jchodera/kinodata
Collection of scripts / notebooks to reliably select datasets
jchodera/kinoml
Structure-informed machine learning for kinase modeling
jchodera/nglview
Jupyter widget to interactively view molecular structures and trajectories
jchodera/open-data-registry
A registry of publicly available datasets on AWS
jchodera/openmm-feedstock
A conda-smithy repository for openmm.
jchodera/ParmEd
Parameter/topology editor and molecular simulator
jchodera/plipify
jchodera/pymbar-feedstock
A conda-smithy repository for pymbar.
jchodera/QCFractal
A distributed compute and database platform for quantum chemistry.
jchodera/sams_sampling
This is a repo that is trying to enhance sampling with SAMSSampler from YANK.
jchodera/staged-recipes
A place to submit conda recipes before they become fully fledged conda-forge feedstocks
jchodera/timemachine
Differentiate all the things!
jchodera/yank-examples
Examples for use of YANK - getyank.org