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mindsdb

In-Database Machine Learning

mmpdb

A package to identify matched molecular pairs and use them to predict property changes.

mmseqs2

MMseqs2: ultra fast and sensitive search and clustering suite

mol_frame

Chemical Structure Handling for Pandas DataFrames

molcloud

Make a bunch of molecules

molecule-generation

Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation

moleculekit

MoleculeKit: Your favorite molecule manipulation kit

molfinder

mols2grid

Interactive chemical viewer for 2D structures of small molecules

msmbuilder

:building_construction: Statistical models for biomolecular dynamics :building_construction:

nglview

Jupyter widget to interactively view molecular structures and trajectories

ommprotocol

A command line application to launch molecular dynamics simulations with OpenMM

opencadd

A Python library for structural cheminformatics

openfold

Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2

openmm

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

openmm-atmmetaforce-plugin

An OpenMM plugin that implements the Alchemical Transfer Potential

optuna

A hyperparameter optimization framework

pandas_exercises

Practice your pandas skills!

pdb2pqr

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

plumed2

Development version of plumed 2

pmx

Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

pocket2mol

Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets

practicalcheminformatics

prody

A Python Package for Protein Dynamics Analysis

protein-ligand-benchmark

Protein-Ligand Benchmark Dataset for Free Energy Calculations

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).

py-rcsb_db

RCSB Python Database Utility Classes

pyautofep

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

pybiomed

machine learning, molecular descriptor

pymol-script-repo

Collected scripts for Pymol