Incorporating specificity into optimization: evaluation of SPA using CSAR 2014 and CASF 2013 benchmarks

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• 作者：Zhiqiang Yan ; Jin Wang
• 关键词：Scoring function ; Protein–ligand interaction ; Binding specificity ; Binding affinity ; SPA ; CASF ; CSAR
• 刊名：Journal of Computer-Aided Molecular Design
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：30
• 期：3
• 页码：219-227
• 全文大小：743 KB
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• 作者单位：Zhiqiang Yan (1)
  Jin Wang (1) (2)
  
  1. State Key Laboratory of Electroanalytical Chemistry Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, Jilin, China
  2. Department of Chemistry and Physics, State University of New York at Stony Brook, Stony Brook, NY, 11794-3400, USA
  
• 刊物类别：Chemistry and Materials Science
• 刊物主题：Chemistry
  Physical Chemistry
  Computer Applications in Chemistry
  Animal Anatomy, Morphology and Histology
  
• 出版者：Springer Netherlands
• ISSN：1573-4951

文摘

Scoring functions of protein–ligand interactions are widely used in computationally docking software and structure-based drug discovery. Accurate prediction of the binding energy between the protein and the ligand is the main task of the scoring function. The accuracy of a scoring function is normally evaluated by testing it on the benchmarks of protein–ligand complexes. In this work, we report the evaluation analysis of an improved version of scoring function SPecificity and Affinity (SPA). By testing on two independent benchmarks Community Structure-Activity Resource (CSAR) 2014 and Comparative Assessment of Scoring Functions (CASF) 2013, the assessment shows that SPA is relatively more accurate than other compared scoring functions in predicting the interactions between the protein and the ligand. We conclude that the inclusion of the specificity in the optimization can effectively suppress the competitive state on the funnel-like binding energy landscape, and make SPA more accurate in identifying the “native” conformation and scoring the binding decoys. The evaluation of SPA highlights the importance of binding specificity in improving the accuracy of the scoring functions.