jchodera

statmech-for-biochemists

A primer on statistical mechanics for biochemists

latex-cv

Example showing how LaTeX can be used to produce a nice-looking curriculum vitae (CV).

jacs-dataset-analysis

Re-analysis of the Schrödinger JACS dataset

alchemical-best-practices

Best practice document for alchemical free energy calculations going to livecoms journal

ambertools-feedstock

A conda-smithy repository for ambertools.

benchmarksets

Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards

Chem456

Web site for Chem 456 - Computational Biochemistry and Drug Design

clusterutils-feedstock

A conda-smithy repository for clusterutils.

conda-forge-pinning-feedstock

A conda-smithy repository for conda-forge-pinning.

covid

MolSSI SARS-CoV-2 Biomolecular Simulation Data and Algorithm Store

experiments-binding-affinity

fah_prep

suite of functions to prepare simulations (docking, free energy) for use with folding at home.

fragmenter-manuscript

freeenergyframework

Package for consistent reporting of relative free energy results

jdcthesis

John Chodera's PhD thesis latex source

kinodata

Collection of scripts / notebooks to reliably select datasets

kinoml

Structure-informed machine learning for kinase modeling

nglview

Jupyter widget to interactively view molecular structures and trajectories

open-data-registry

A registry of publicly available datasets on AWS

openmm

OpenMM is a toolkit for molecular simulation using high performance GPU code.

openmm-feedstock

A conda-smithy repository for openmm.

ParmEd

Parameter/topology editor and molecular simulator

plipify

pymbar-feedstock

A conda-smithy repository for pymbar.

QCFractal

A distributed compute and database platform for quantum chemistry.

sams_sampling

This is a repo that is trying to enhance sampling with SAMSSampler from YANK.

simple-simulate-complex

Simple protein-ligand complex simulation with OpenMM

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

timemachine

Differentiate all the things!

yank-examples

Examples for use of YANK - getyank.org