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Simple solvation potential for coarse‐grained models of proteins
Author(s) -
Bhattacharyay A.,
Trovato A.,
Seno F.
Publication year - 2007
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.21291
Subject(s) - solvation , simple (philosophy) , atom (system on chip) , chemistry , representation (politics) , biological system , implicit solvation , statistical physics , computational chemistry , set (abstract data type) , chemical physics , computer science , molecule , physics , biology , philosophy , organic chemistry , epistemology , politics , political science , law , embedded system , programming language
We formulate a simple solvation potential based on a coarsed‐grained representation of amino acids with two spheres modeling the C α atom and an effective side‐chain centroid. The potential relies on a new method for estimating the buried area of residues, based on counting the effective number of burying neighbors in a suitable way. This latter quantity shows a good correlation with the buried area of residues computed from all atom crystallographic structures. We check the discriminatory power of the solvation potential alone to identify the native fold of a protein from a set of decoys and show the potential to be considerably selective. Proteins 2007. © 2007 Wiley‐Liss, Inc.