shiyx409

protwis

Protwis is the backbone of the GPCRdb. The GPCRdb contains reference data, interactive visualisation and experiment design tools for G protein-coupled receptors (GPCRs).

analysis_libraries_chapter

Analysis libraries for molecular trajectories: a cross-language synopsis

Free-Wilson

An implementation of the Free-Wilson SAR analysis method using the RDKit

neutromeratio

Tautomer ratios in solution

parKVFinder

parKVFinder: thread-level parallel KVFinder

resp

A. Alenaizan's restricted electrostatic potential (RESP) plugin to Psi4

Potential_solver

A Python module for solving electrostatic potential of a distribution of point charges using periodic boundary conditions.

esp-surface-generator

Generate electrostatic potential surfaces using the output from Astex's ESP_DNN method

ProteinDesignPlugin

pymol-color-alphafold

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

PyMolSAR

A Python toolkit to compute molecular features and predict activities and properties of small molecules

remd_temperature

Python library to query web server with temperature generator for REMD-simulations

CheS-Mapper

torsional-diffusion

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.

tutorials

Various tutorials about MD setup and analysis, protein-ligand docking, machine learning and lots of other interesting things.

molcloud

Make a bunch of molecules

moviepy

Video editing with Python

ScaffoldGraph

ScaffoldGraph is an open-source cheminformatics library, built using RDKit and NetworkX, for the generation and analysis of scaffold networks and scaffold trees.

e3_diffusion_for_molecules

arpeggio

Calculation of interatomic interactions in molecular structures

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

DROIDS-2.0---free-software-for-comparative-protein-dynamics

DROIDS v2.0 final beta release is done. It now incorporates the ability to create and analyze mutant model dynamics. New pipelines for protein-ligand and DNA-protein interaction and multi-chain complexes are supported. IMPORTANT: DROIDS v3.0 is now available here https://github.com/gbabbitt/DROIDS-3.0-comparative-protein-dynamics

pytraj

Python interface of cpptraj

pyrite

core repository

mdtraj

An open library for the analysis of molecular dynamics trajectories

cpptraj

Biomolecular simulation trajectory/data analysis.

pymod

PyMod 3 - sequence similarity searches, multiple sequence/structure alignments, and homology modeling within PyMOL.

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

protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations