Simplification of protein representation from the contact potentials between residues

2000/10/19 by Jun Wang, Wei Wang, Wang, Jun +1
Biochemistry, Genetics and Molecular Biology · Chemistry · Computer Science · Physics and Astronomy · #Computational Drug Discovery Methods #Molecular spectroscopy and chirality #Protein Structure and Dynamics #cond-mat.soft #cond-mat.stat-mech #q-bio

paper · pdf · doi:10.48550/arxiv.cond-mat/0010288

10 pages, 5 figures, submitted to PRL

arxiv created 2000/10/19 · arxiv updated 2009/11/30

Abstract

Based on the concept of energy landscape a picture of the mismatch between the reduced interaction matrix of residues and the matrix of statistical contact potentials is presented. For the Miyazawa and Jernigan (MJ) matrix, rational groupings of 20 kinds of residues with minimal mismatches under the consideration of local minima and statistics on correlation between the residues are studied. A hierarchical tree of groupings relating to different numbers of groups N is obtained, and a plateau around N=8∼ 10 is found, which may represent the basic degree of freedom of the sequence complexity of proteins.

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