choderalab Goto Github PK

openmmenergycomparisons

Comparisons of energies and forces between OpenMM and other packages

openmmmcmc

A general Markov chain Monte Carlo framework for OpenMM.

openmmtools

A batteries-included toolkit for the GPU-accelerated OpenMM molecular simulation engine.

openmoltools

An open set of tools for automating tasks relating to small molecules

paper-microfluidics

Experiments with paper-based microfluidics

papers-and-grants

YAML database of papers and grants from the Chodera lab

pdbanalyzer

PDB Metal Stats

pdbanalyzer-results

Results of PDB-wide metal analyses

pdbfinder

a collection of scripts and files to help in PDB retrieval for various projects

peanut

peptide-design

Design selective peptides targeting SH2 domains

perses

Experiments with expanded ensembles to explore chemical space

perses-barnase-barstar-paper

Contains scripts and data for the perses barnase barstar paper

perses-orion

Simple example of running perses on Orion

persesatfoldingathome

persesmoviemaker

Move making tools for perses

pimento

Protein methyltransferases

pinot

Probabilistic Inference for NOvel Therapeutics

pisco

Probabilistic Inference for Shape, Conformation, and Organization of Macromolecular Systems

plasmidlibrarytools

PlasmidLibraryTools

plipify

Choderalab fork of plipify package

printable-3d-parts

Useful parts that can be 3D printed.

protons

OpenMM testbed for constant-pH methodologies.

protons-templates

Templates for running protons simulations

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

pymbar-datasets

pymbar-examples

Examples of applications of pymbar to various problems in simulation and experiment

pyopenmm

qmlify

qmmm-hydration

QM/MM hydration free energy playground