talagayev

tauRAMD

Computation of the drug-target relative residence times from RAMD simulations

openmmtools

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

MDANCE

MDANCE is a flexible n-ary clustering package for all applications.

molearn

protein conformational spaces meet machine learning

pysoftk

Python program for modelling and simulating polymers.

mdpath

MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral angle movements throughout an MD simulation.

DockM8

All in one Structure-Based Virtual Screening workflow based on the concept of consensus docking.

openfe

The Open Free Energy toolkit

pdbfixer

PDBFixer fixes problems in PDB files

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

MDonatello

2D small molecule visualization for MDAnalysis

martini_openmm

Smiles-TO-iUpac-Translator

Transformer based SMILES to IUPAC Translator

ProLIF

Interaction Fingerprints for protein-ligand complexes and more

asapdiscovery

Toolkit for open antiviral drug discovery by the ASAP Discovery Consortium

stormm

DECIMER-Image-to-SMILES

The repository contains the network and the related scripts for encoder-decoder based Chemical Image Recognition

CADD_Vault

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

QSPRpred

A tool for creating Quantitative Structure Property/Activity Relationship (QSPR/QSAR) models.

black

The uncompromising Python code formatter

OpenMMDL

Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes

kinoml

Structure-informed machine learning for kinase modeling

dynophores

Dynamic pharmacophore modeling of molecular interactions

europin-website

streamd

Automate MD associated calculations

gromacs-ramd

Random Acceleration Molecular Dynamics in GROMACS

deeptime

Python library for analysis of time series data including dimensionality reduction, clustering, and Markov model estimation

teachopencadd

TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data

openmm-setup

An application for configuring and running simulations with OpenMM