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absolv_test

Trying out absolv

alchemical-analysis

An open tool implementing some recommended practices for analyzing alchemical free energy calculations

autodock_vina

A fork of AutoDock Vina (http://vina.scripps.edu). Updated to boost 1.70. Simplified the build process.

bieniekmateusz.github.io

blog.github.io

fe_input_tests

SOMD and OMMT starting files

fegrow-case-sarscov2-3tor

RBFE input files for the reproduction of the study case sarscov2-3toR in rgroup package.

fegrow-feedstock

A conda-smithy repository for fegrow.

fesetup

A tool for setting up free energy simulations.

forcebalance

Systematic force field optimization.

freesasa

C-library for calculating Solvent Accessible Surface Areas

freesasa-python

FreeSASA Python Module

gal

Google active learning

googlehashcode

A collection of 'solutions' to Google Hashcodes.

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mdscripts

openff-toolkit

The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

openmm-ml

High level API for using machine learning models in OpenMM simulations

protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations

protein-ligand-openmm-workflow

Workflow for an MD simulation of a protein-ligand complex in water with openmm

publications

Scripts and files related to the publications

pydockingorg

Rewritten version of Matteo Ferla's unofficial python API to SmallWorld

pymbar

Python implementation of the multistate Bennett acceptance ratio (MBAR)

pymbar-examples

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

pymol-mdanalysis

Exploratory PyMOL-MDAnalysis molecular visualization system.

pymol-testing

PyMOL Testing Framework

pyqcprot

Python implementation of the fast rmsd and optimal rotation matrix method by Douglas Theobald and Pu Liu

python_smallworld_api

An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)

qube-somd-paper

qubekit

Quantum Mechanical Bespoke Force Field Derivation Toolkit