HTMD is a molecular-specific programmable environment to prepare, handle, simulate, visualize and analyse molecular systems. HTMD is based on Python, so scientists can easily extend it to their needs. With HTMD is possible to do very complex protocols in just few lines.
In a single script, it is possible to plan an entire computational experiment, from manipulating PDBs, building, executing and analysing simulations, computing Markov state models, kinetic rates, affinities and pathways.
HTMD has been successfully used for FBDD, for GPCR ligand binding, Antibody structural analysis and more.