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Computation of conformational entropy from protein sequences using the machine‐learning method—Application to the study of the relationship between structural conservation and local structural stability
Author(s) -
Huang ShaoWei,
Hwang JennKang
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20462
Subject(s) - structural stability , entropy (arrow of time) , sequence (biology) , conformational entropy , protein structure , protein folding , structural alignment , computation , stability (learning theory) , support vector machine , computer science , artificial intelligence , biological system , algorithm , chemistry , peptide sequence , sequence alignment , machine learning , biology , physics , molecule , thermodynamics , biochemistry , engineering , structural engineering , organic chemistry , gene
A complete protein sequence can usually determine a unique conformation; however, the situation is different for shorter subsequences—some of them are able to adopt unique conformations, independent of context; while others assume diverse conformations in different contexts. The conformations of subsequences are determined by the interplay between local and nonlocal interactions. A quantitative measure of such structural conservation or variability will be useful in the understanding of the sequence–structure relationship. In this report, we developed an approach using the support vector machine method to compute the conformational variability directly from sequences, which is referred to as the sequence structural entropy. As a practical application, we studied the relationship between sequence structural entropy and the hydrogen exchange for a set of well‐studied proteins. We found that the slowest exchange cores usually comprise amino acids of the lowest sequence structural entropy. Our results indicate that structural conservation is closely related to the local structural stability. This relationship may have interesting implications in the protein folding processes, and may be useful in the study of the sequence–structure relationship. Proteins 2005. © 2005 Wiley‐Liss, Inc.