期刊
JOURNAL OF COMPUTATIONAL CHEMISTRY
卷 41, 期 1, 页码 14-20出版社
WILEY
DOI: 10.1002/jcc.26070
关键词
coarse-graining; optimal CG sites; internal cluster validation index; CH index; SC index
资金
- National Natural Science Foundation of China [21773065, 21433004, 21673185, 21873078]
- Nanyang Technological University Startup Grant [M4081842]
- Singapore Ministry of Education Academic Research fund Tier 1 [RG31/18]
- Singapore Ministry of Education Academic Research fund Tier 2 [MOE2018-T2-1-033]
- NYU-ECNU Center for Computational Chemistry at NadenylateYU Shanghai
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. (c) 2019 Wiley Periodicals, Inc.
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