PMX is a free, open-source tool for setting up and analysing alchemical free-energy calculations with GROMACS. It automates the generation of hybrid structures and molecular topologies for studying mutations and ligand-binding changes, supporting applications in biomolecular research and computer-aided drug discovery.

HADDOCK (High Ambiguity Driven protein–protein DOCKing) is a data-driven computational platform developed by Alexandre Bonvin and the Computational Structural Biology group at Utrecht University. It predicts and models biomolecular complexes—such as protein–protein, protein–DNA, and protein–RNA interactions—by integrating experimental data with molecular modeling and docking methods.

A premier, deeply granular performance analysis tool. Computer scientists use it to optimize thread execution, memory access, and vectorization to ensure their code is extracting maximum theoretical performance from the underlying CPU/GPU architecture.