AnalysisFMO Toolkit: A PyMOL Plugin for 3D-Visualization of Interaction Energies in Proteins (3D-VIEP) Calculated by the FMO Method

Interresidue and ligand/substrate-residue interactions in a biomacromolecular system such as drug target protein variously correlated with structure, function, and bioactivity of the system. Reliable theoretical interaction analysis with a ligand/substrate has given us fruitful information to identify the key residue and theoretically design novel high potent candidates. The interfragment interaction energies can be calculated appropriately under the FMO scheme based on the first-principles (electronic) calculations. Analysis tool of the FMO method is very useful by visualizing and rendering analysis of the results in protein structure: 3D-visualization of interaction energies in proteins (3D-VIEP). We have also developed the toolkit “AnalysisFMO” to perform the 3D-VIEP method, which can assist in analyzing the FMO results generated by quantum-chemical packages such as GAMESS, PAICS, and ABINIT-MP. AnalysisFMO consists of two separate tools, RbAnalysisFMO and the PyMOL plugins by Ruby and Python programs, respectively. The first tool can extract interfragment interaction energies (IFIEs) or pair interaction energies (PIEs) from the FMO output file, and the second tool enables to visualize IFIEs or PIEs in the target system together with structures on a window of PyMOL program.