Provides a set of scripts for protein mutagenesis and activation free energy calculation via the empirical valence bond method.
SEPPO is a set of python scripts built from the OpenMM API that aid in the process of rational enzyme design. SEPPO includes the capacity for generating mutant enzymes from a wild type structure and simulating how these mutations affect catalysis by using the empirical valence bond method to predict changes in activation free energy. SEPPO can also be used to study the free energy of various chemical reactions using molecular dynamics.
SEPPO uses the functionality of a number of different SimTK projects including: OpenMM, Yank, pyMBAR, and ForceBalance.