Comparison of binding affinity evaluations for FKBP ligands with state-of-the-art computational methods: FMO, QM/MM, MM-PB/SA and MP-CAFEE approaches

Chem-Bio Informatics Journal

藤谷 �?章⁴  勝山 マリコ³  田中 成典²  三井 崇志³  沖本 憲明¹  泰地 真弘人¹  谷田 義明⁴  渡邉 博文²  長谷�? 亜樹¹ 

[1] 理化学研究所システム計算生物学研究チーム;神戸大学大学院工学研究科;富士通株式会社;株式会社富士通研究所

关键词: Protein-ligand binding affinity;    タンパク質リガンド結合能;    Fragment molecular orbital method;    フラグメント分子軌道法（FMO法）;    QM/MM method;    QM/MM法;    MM-PB/SA method;    MM-PB/SA法;    MP-CAFEE method;    MP-CAFEE法;    FKBP;    FK506結合タンパク質（FKBP）;   

DOI  :  10.1273/cbij.10.32

学科分类：生物化学/生物物理

来源: Chem-Bio Informatics Society

【 摘 要 】

References(46)Cited-By(5)We compared binding affinity evaluations for 10 FKBP ligands with such state-of-the-art computational methods as FMO, QM/MM, MM-PB/SA, and MP-CAFEE. For the FKBP ligands, we confirmed that each method could provide good correlations between the experimental and computational binding affinities.From the calculated results, we discussed the importance of solvation effect and structural sampling for these methods in detail. In addition, we argued the issue of computational time and present arguments on the future perspective of the computational binding affinity evaluations.

【 授权许可】

Unknown