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lintools

Python script that creates 2D protein-ligand interaction images

mcdock

McDock: Simple Monte Carlo docking algorithm in C++

md-analysis-tools

scripts for analyzing molecular dynamics trajectories using VMD

md-ifp

MD trajectory analysis using protein-ligand Interaction Fingerprints

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mgssl

Official implementation of NeurIPS'21 paper"Motif-based Graph Self-Supervised Learning for Molecular Property Prediction"

modedock

Protein ligand docking based on multiple-objective differential evolution algorithm

mols2grid

Interactive molecule viewer for 2D structures

mpi-vina

An MPI based parallel implementation of Autodock Vina

msmpathfinder

Finding pathways from an Markov State Model

multiobj-rationale

Multi-Objective Molecule Generation using Interpretable Substructures (ICML 2020)

mutatex

scripts and facilities for in-silico mutagenesis with FoldX

omegafold

OmegaFold Release Code

openfold

Trainable PyTorch reproduction of AlphaFold 2

openmm_bedam_plugin

A plugin to add BEDAM binding free energy module to OpenMM

openmm_sdm_plugin

OpenMM plugin to implement single-decoupling method in alchemical free energy calculations

opls-aam

Implementing OPLS-AA/M Force field in OpenMM from CHARMM formatted parameter files

opls-aam_for_gromacs

Gromacs Implementation of OPLS-AAM Force field

oplsidpsff

packmol

Packmol - Initial configurations for molecular dynamics simulations

paprika

Advanced toolkit for binding free energy calculations

paradocks

Framework for molecular docking with population-based metaheuristics

pharmd

MD pharmacophores and virtual screening

plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

pocket2mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

protein-ligand-openmm-workflow

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

proteinmpnn

Code for the ProteinMPNN paper

protocaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

psiresp

RESP with inter- and intra-molecular constraints in Psi4.