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.

FEniCSx is a popular open-source (LGPLv3) computing platform for solving partial differential equations (PDEs).

NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters.

CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.

LAMMPS is a classical molecular dynamics (MD) code.

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.