The Database Toolkit for Python

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Standardized data set for machine learning of protein structure

Working with molecular structures in pandas DataFrames

Collected scripts for Pymol

Parameter/topology editor and molecular simulator

Interaction Fingerprints for protein-ligand complexes and more

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

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

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

Benchmarking framework for protein representation learning. Includes a large number of pre-training and downstream task datasets, models and training/task utilities. (ICLR 2024)

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

Geometry optimization code that includes the TRIC coordinate system

A repository for quantum chemistry basis sets

🏗️ Statistical models for biomolecular dynamics 🏗️

Generative modeling of molecular dynamics trajectories

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

Code for ColabDock paper

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

predicting peptide-protein interactions

Experimental and calculated small molecule hydration free energies

clusterize molecular dynamic trajectories (amber, gromacs, charmm, namd, pdb...)

binding free energy estimator 2

Molecular AutoEncoder in PyTorch

A PyMOL Plugin for calculating docking box for LeDock, AutoDock and AutoDock Vina.