Links to software that has been used in CCPBioSim training events. We do not maintain or develop these tools.

Amber - a molecular dynamics program

BioSimSpace - a workflow tool

GROMACS - a molecular dynamics program

ProDy - a free and open-source Python package for protein structural dynamics analysis.

propka - a tool for calculating the pKa of ionizable groups

reduce - a tool for adding hydrogens to pdb structures