Development of the molecular modeling program for quantum chemical calculation on proteins

Abstract

Protein Data Bank (PDB) is the common data source of protein geometries. However, the most structures are determined by X-ray diffraction (about 85 percents) which causes the lack of hydrogen atoms positions. In addition, distorted and/or indistinct geometries are often observed in PDB data. It is necessary to check the validity to PDB data for simulations on proteins, in particular molecular orbital (MO) calculations. Since protein has huge and complicated structure, automatic support is indispensable. In this study, we developed a new molecular modeling program for PDB data to support simulations on proteins. Our program has functions of hydrogen addition, checking the structural validity, amino acid substitution (point mutation) and chemical modification to PDB. Referring the PDB hetero group dictionary, the modeling such as hydrogen addition is easily achieved to proteins containing hetero groups which have a large variety of bonding patterns. The program was coded by the object oriented language C++ and developed as standalone library.