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Empirical potential function for simplified protein models: Combining contact and local sequence–structure descriptors
Author(s) -
Zhang Jinfeng,
Chen Rong,
Liang Jie
Publication year - 2006
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.20809
Subject(s) - decoy , protein structure prediction , sequence (biology) , function (biology) , biological system , protein folding , statistical potential , protein structure , folding (dsp implementation) , chemistry , algorithm , computer science , biology , engineering , biochemistry , receptor , evolutionary biology , electrical engineering
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only C α or backbone atoms are attractive because they enable efficient search of the conformational space. We show residue‐specific reduced discrete‐state models can represent the backbone conformations of proteins with small RMSD values. However, no potential functions exist that are designed for such simplified protein models. In this study, we develop optimal potential functions by combining contact interaction descriptors and local sequence–structure descriptors. The form of the potential function is a weighted linear sum of all descriptors, and the optimal weight coefficients are obtained through optimization using both native and decoy structures. The performance of the potential function in a test of discriminating native protein structures from decoys is evaluated using several benchmark decoy sets. Our potential function requiring only backbone atoms or C α atoms have comparable or better performance than several residue‐based potential functions that require additional coordinates of side‐chain centers or coordinates of all side‐chain atoms. By reducing the residue alphabets down to size 10 for contact descriptors, the performance of the potential function can be further improved. Our results also suggest that local sequence–structure correlation may play important role in reducing the entropic cost of protein folding. Proteins 2006. © 2006 Wiley‐Liss, Inc.