P02-12
Preprocessing of FMO calculations and practical visualization of interaction energies for drug design
Hirofumi WATANABE *1, Yuji TANAKAMARU2
1WithMetis Co., Ltd.
2Malo21st
( * E-mail: h.watanabe314@gmail.com )
Based on quantum mechanics, the fragment molecular orbital (FMO) method provides computational evaluations of protein-ligand interactions through inter-fragment interaction energy (IFIE) analysis and its decomposition analysis (PIEDA).
We have been developing an FMO-based drug design software package called Q-AIR. First, Grinder, one of the modules of Q-AIR, preprocesses FMO calculations. This module has several preprocess functions, such as adding missing atoms in protein and protonation of both protein and ligand, as well as minimization near complemented regions. We will discuss the influence of protonation or complementation and appropriate preprocessing for obtaining a better correlation between activities and interactions. Next, Flair viewer in Q-AIR provides visual analysis between a ligand and surrounding amino acid residues and insights for modifications of compound structures. At the last CBI annual meeting, we reported adding a 2D diagrammatic depiction while keeping information on the 3D positions and distances of amino acid residues surrounding the ligand. This year’s update for the viewer is the improvement of the algorithm of 2D-diagrammatic depiction. With this improvement, we can get stable and easy-to-understand depictions of any situation regarding a ligand and its surrounding residues.