ProtoMS

ProtoMS is a complete Monte Carlo biomolecular simulation program designed to calculate relative free energies (including relative binding free energies) on large systems. It supports FEP, FDTI, RETI, umbrella sampling, and can run using large system (hundreds of thousands of atoms), using either explicit water models or the implicit GBSA water model. ProtoMS supports a large range of simulations that are useful for rational drug design, including the calculation of binding affinity of water molecules (useful for water mapping, e.g. see "Classification of Water Molecules in Protein Binding Sites", DOI: 10.1021/ja066980q).

ProtoMS has been used to produce the science in multiple publications. This website supports the future development of the code, and its continued use. ProtoMS is stable, and so development is limited to maintenance. The primary developers have moved on to the development of the sucessor of ProtoMS, called Sire.

If you want to download ProtoMS, please visit protoms.googlecode.com and either download either a released version (from the "Downloads" section) or feel free to download a (possibly broken!) version from the subversion repository.

ProtoMS comes with a tutorial (in the "tutorials" directory, file ProtoMS.htm). A copy of this tutorial can also be found here. ProtoMS was also used in a workshop teaching how to calculate relative hydration and binding free energies. The workshop, together with all materials, can be found here.

If you want to ask questions or get help, then please join the ProtoMS Users mailing group.