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Positioning hydrogen atoms by optimizing hydrogen‐bond networks in protein structures
Author(s) -
Hooft Rob W.W.,
Sander Chris,
Vriend Gerrit
Publication year - 1996
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/(sici)1097-0134(199612)26:4<363::aid-prot1>3.0.co;2-d
Subject(s) - hydrogen bond , chemistry , molecule , crystallography , crystal structure , force field (fiction) , protein structure , protein crystallization , hydrogen , docking (animal) , molecular dynamics , biomolecular structure , chemical physics , computational chemistry , physics , biochemistry , organic chemistry , medicine , nursing , quantum mechanics , crystallization
A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, sidechain conformations of His, Gln, and Asn residues are allowed to change their last χ angle by 180° to compensate for crystallographic misassignments. Crystal structure symmetry is taken into account where appropriate. The results can have significant implications for molecular dynamics simulations, protein engineering, and docking studies. The largest impact, however, is in protein structure verification: over 85% of protein structures tested can be improved by using our procedure. Proteins 26:363–376 © 1996 Wiley‐Liss, Inc.