ProtoMS: 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. 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.

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