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Partition of protein solvation into group contributions from molecular dynamics simulations
Author(s) -
Morreale Antonio,
de la Cruz Xavier,
Meyer Tim,
Gelpí Josep Lluís,
Luque F. Javier,
Orozco Modesto
Publication year - 2004
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.20292
Subject(s) - solvation , molecular dynamics , statistical physics , partition (number theory) , representation (politics) , computational chemistry , chemistry , implicit solvation , basis (linear algebra) , flexibility (engineering) , partition coefficient , molecule , chemical physics , thermodynamics , physics , mathematics , organic chemistry , geometry , combinatorics , politics , political science , law , statistics
Linear response theory coupled to molecular dynamics simulations with an explicit solvent representation is used to derive fractional contributions of amino acid residues to the solvation of proteins. The new fractional methods developed here are compared with standard approaches based on empirical 1D and 3D statistical potentials, as well as with estimates obtained from the analysis of classical molecular interaction potentials. The new fractional methods, which have a clear physical basis and explicitly account for the effects due to protein structure and flexibility, provide an accurate picture of the contribution to solvation of different regions of the protein. Proteins 2005. © 2004 Wiley‐Liss, Inc.