Development of atomic charges for proteins by using the linear regression method based on canonical molecular orbital calculation

• KIM Taehwan

  東京大学大学院　工学系研究科

• HIRANO Toshiyuki

  東京大学生産技術研究所　機械・生体系部門

• SATO Fumitoshi

  東京大学生産技術研究所革新的シミュレーション研究センター

Bibliographic Information

Other Title

• カノニカル分子軌道計算に基づく線形回帰法を用いたタンパク質原子電荷の開発
• カノニカル ブンシ キドウ ケイサン ニ モトズク センケイ カイキホウ オ モチイタ タンパクシツ ゲンシ デンカ ノ カイハツ

Abstract

The RESP charge has been proposed for the purpose of reproducing the electrostatic potential （ESP） of molecules and widely used for the molecular mechanics or molecular dynamics simulation. Because the cost of the RESP charge determination by using full QM calculation is high, the protein RESP charge is substituted by the combination of parameterized RESP charge for each amino acid residue. In this study, we have developed the atomic charge calculation method which reproduce intrinsic ESP based on the canonical molecular orbital calculation of the entire protein and improved the quality of atomic charge. In addition to RESP charge followed by the original definition, the various atomic charges of protein were proposed by applying the linear regression method to the atomic charge model with keeping the property of accurate ESP reproductivity.

Journal

• SEISAN KENKYU

  SEISAN KENKYU 68 (3), 213-217, 2016

  Institute of Industrial Science The University of Tokyo

Details

• CRID: 1390001204062574720
• NII Article ID: 130005153090
• NII Book ID: AN00127075
• DOI: 10.11188/seisankenkyu.68.213
• ISSN: 18812058
• ISSN: 0037105X
• NDL BIB ID: 027482104
• Web Site: http://id.ndl.go.jp/bib/027482104
• Web Site: https://ndlsearch.ndl.go.jp/books/R000000004-I027482104
• Text Lang: en
• Data Source:
  • JaLC
  • NDL
  • CiNii Articles
  • KAKEN
• Abstract License Flag: Disallowed