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autoprotocol-python

Python library for generating Autoprotocol

bettermedtime

A tool for optimizing when to take multiple drugs to reduce side effects

biopython

Official git repository for Biopython (converted from CVS)

cardsreader

CARDS-Reader: Methods to analyze CARDS data

cbang

C! (cbang) is a library of cross-platform C++ utilities.

cdk

CDK2/CDK4 Folding@home simulations

covid

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

deeptime

Deep learning meets molecular dynamics.

ensembler

Software pipeline for automating omics-scale protein modeling and simulation setup.

enspara

Modeling molecular ensembles with scalable data structures and parallel computing

erk_reconstruction

ERK ancestral reconstruction

fahmunge

Tools for Munging Folding@Home datasets

ffconv

Amber --> OpenMM ffxml conversion

keras

Deep Learning library for Python. Convnets, recurrent neural networks, and more. Runs on Theano and TensorFlow.

mdtraj

A modern, open library for the analysis of molecular dynamics trajectories

molprobity

Protein and nucleic acid validation service

msm_play

msmbuilder

Statistical models for biomolecular dynamics

mta

Scrape & analyze MTA arrival times

nglview

IPython widget to interactively view molecular structures and trajectories

notes

For making notes and storing some asap code for my current work

openmm

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

openmmexampleplugin

An example of how to write a plugin for OpenMM

openmoltools

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

parmed

Parameter/topology editor and molecular simulator

pdb-tools

Set of utility scripts to manipulate PDB files

pdbfixer

PDBFixer fixes problems in PDB files

pdbtools

A set of tools for manipulating and doing calculations on wwPDB macromolecule structure files

pyemma

Emma's Markov Model Algorithms

pytraj

Interactive data analysis for molecular dynamics simulations