ProteinEditor: Integrated Environment for Quantum Chemical Calculation System for Proteins

Abstract

We have developed the quantum chemical calculation system for proteins based on the density functional method program ProteinDF. This system is composed of five subsystems: "Automatic computations", "Geometry optimization and ab initio molecular dynamics (MD) calculation (Quantum dynamics)", "Calculations on very large-sized proteins", "Database of protein wavefunctions", and "Integrated environment, ProteinEditor". In this study, we will report the development of ProteinEditor subsystem. In all-electron calculations on proteins, the data size is huge and the simulation becomes complex. Therefore, an interactive and easy control by the user is indispensable. To reduce these problems, ProteinEditor contains a graphical user interface (GUI) to support the all-electron semi-automatic calculation method for proteins (QCLO method). The structural interaction representation functions cooperated with the high-performance molecular graphics can assist the safe quantum chemical calculation. We also implemented the functions of hydrogen addition, the amino acid substitution (point mutation) and checking the structural validity of proteins in PDB format. This work will guarantee the easy and safe achievement of quantum chemical simulation of proteins