Monte Carlo Biomolecular Free Energy Simulation Program

ProtoMS is a complete Monte Carlo biomolecular simulation program which is able to perform a series of different simulations, such as relative and absolute free energy calculations and water placement with GCMC and JAWS methodology. ProtoMS is mainly designed to work with explicit solvent, but it contains the necessary capabilities to perform simulations with implicit GBSA water model.

Both the set up of the simulations and the analysis of the produced data have been highly automated, so running and analysing one of the standard simulations with ProtoMS should be very easy. There are also further advanced options that provide all the desired flexibility, so that you can simulate exactly what you want.

Please, use the navigation bar available to find out how to download ProtoMS, the publications whose research has been generated with this software, more on its tutorials and manual, or the workshops that regularly take place. If you want to ask questions or get help, then please get in contact.

Current version of ProtoMS 3.2.0