Protein-Protein Interaction Modelling with the Fragment Molecular Orbital Method

Abstract

Fragment molecular orbital (FMO) method enables ab initio quantum-chemical calculations for biomolecular systems with high accuracy and moderate computational cost. Through this analysis we can evaluate the inter-fragment interaction energies (IFIEs) that provide useful measures for effective interactions between the fragments representing amino-acid residues and ligand molecules. Here I describe how to prepare the input structures and perform the FMO calculations for protein-protein complex system. In addition to the pre-processing, some useful tools for the post-processing analysis are also illustrated.

Keywords: Fragment molecular orbital (FMO) method; Inter-fragment interaction energy (IFIE); Measles virus hemagglutinin (MVH); Protein–protein interaction (PPI); Signaling lymphocyte activation molecule (SLAM).