method-statistics

Cryptic binding pocket discovery from conformational ensembles. Open-source, reproducible, size-robust benchmarks against fpocket, PocketMiner and CryptoBench.

Python implementation of the multistate Bennett acceptance ratio (MBAR)

A Python Package for Protein Dynamics Analysis

Experiments with expanded ensembles to explore chemical space

Solvation Structure and Thermodynamic Mapping

A pocket volume analyzer for use in protein modeling.

Computational Crystallography Toolbox

The Open Free Energy toolkit

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

A comprehensive library for computational molecular biology

🚂 Python API for Emma's Markov Model Algorithms 🚂

Official git repository for Biopython (originally converted from CVS)

🏗️ Statistical models for biomolecular dynamics 🏗️

Annotated data.

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

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

scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.

Detect and characterize binding pockets from molecular simulations.

Protein Ligand INteraction Dataset and Evaluation Resource

An open library for the analysis of molecular dynamics trajectories