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

Development version of plumed 2

Python script to convert Alphafold output to collective variable

A Python class for scheduling SLURM jobs

OFFICIAL: AnteChamber PYthon Parser interfacE

A python toolkit for analysing membrane protein-lipid interactions.

AbLang: A language model for antibodies

Swarm-CG: Automatic Parametrization of Bonded Terms in MARTINI-based Coarse-Grained Models of Simple to Complex Molecules via Fuzzy Self-Tuning Particle Swarm Optimization

Automatic MARTINI parametrization of small organic molecules

A hierarchical, component based molecule builder

Trainable PyTorch reproduction of AlphaFold 2

Mapping small-molecules to Martini 3 coarse-grained representations

Martini 3 small-molecule database

Application to assign secondary structure to proteins

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

Describe and apply transformation on molecular structures and topologies

Python implementation of the multistate Bennett acceptance ratio (MBAR)

VMD configuration files