Determining Optimal Coarse‐Grained Representation for Biomolecules Using Internal Cluster Validation Indexes. Issue 1 (30th September 2019)

• Record Type: Journal Article
• Authors: Wu, Zhenliang; Zhang, Yuwei; Zhang, John Zenghui; Xia, Kelin; Xia, Fei
• Is Part Of: Journal of computational chemistry. Volume 41:Issue 1(2020)
• Page Start: 14
• Page End: 20
• Publication Date: 2019-09-30
• Subjects: coarse‐graining -- optimal CG sites -- internal cluster validation index -- CH index -- SC index; Chemistry -- Data processing -- Periodicals; 542.85
• DOI: 10.1002/jcc.26070
• Languages: English
• ISSNs: 0192-8651

Abstract

Abstract : The development of ultracoarse‐grained models for large biomolecules needs to derive the optimal number of coarse‐grained (CG) sites to represent the targets. In this work, we propose to use the statistical internal cluster validation indexes to determine the optimal number of CG sites that are optimized based on the essential dynamics coarse‐graining method. The calculated curves of Calinski‐Harabasz and Silhouette Coefficient indexes exhibit the extrema corresponding to the similar CG numbers. The calculated ratios of the optimal CG numbers to the residue numbers of fine‐grained models are in the range from 4 to 2. The comparison of the stability of index results indicates that Calinski‐Harabasz index is the better choice to determine the optimal CG representation in coarse‐graining. © 2019 Wiley Periodicals, Inc. Abstract : The optimal number of coarse‐grained sites is determined by the maximum of internal cluster validation index.