Taking Water into Account with the Fragment Molecular Orbital Method

Yoshio Okiyama, Kaori Fukuzawa, Yuto Komeiji, Shigenori Tanaka

研究成果: Chapter

3 被引用数 (Scopus)

抄録

This chapter describes the current status of development of the fragment molecular orbital (FMO) method for analyzing the electronic state and intermolecular interactions of biomolecular systems in solvent. The orbital energies and the inter-fragment interaction energies (IFIEs) for a specific molecular structure can be obtained directly by performing FMO calculations by exposing water molecules and counterions around biomolecular systems. Then, it is necessary to pay attention to the thickness of the water shell surrounding the biomolecules. The single-point calculation for snapshots from MD trajectory does not incorporate the effects of temperature and configurational fluctuation, but the SCIFIE (statistically corrected IFIE) method is proposed as a many-body correlated method that partially compensates for this deficiency. Furthermore, implicit continuous dielectric models have been developed as effective approaches to incorporating the screening effect of the solvent in thermal equilibrium, and we illustrate their usefulness for theoretical evaluation of IFIEs and ligand-binding free energy on the basis of the FMO-PBSA (Poisson–Boltzmann surface area) method and other computational methods.

本文言語English
ホスト出版物のタイトルMethods in Molecular Biology
出版社Humana Press Inc.
ページ105-122
ページ数18
DOI
出版ステータスPublished - 2020
外部発表はい

出版物シリーズ

名前Methods in Molecular Biology
2114
ISSN(印刷版)1064-3745
ISSN(電子版)1940-6029

ASJC Scopus subject areas

  • 分子生物学
  • 遺伝学

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