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Predictions of protein flexibility: First‐order measures
Author(s) -
Kovacs Julio A.,
Chacón Pablo,
Abagyan Ruben
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.20151
Subject(s) - dihedral angle , conformal map , flexibility (engineering) , function (biology) , grid , set (abstract data type) , force field (fiction) , biological system , normal mode , deformation (meteorology) , mode (computer interface) , computer science , vibration , algorithm , molecule , statistical physics , mathematics , physics , mathematical analysis , geometry , artificial intelligence , statistics , biology , acoustics , hydrogen bond , programming language , operating system , quantum mechanics , evolutionary biology , meteorology
Abstract The normal modes of a molecule are utilized, in conjunction with classical conformal vector field theory, to define a function that measures the capability of the molecule to deform at each of its residues. An efficient algorithm is presented to calculate the local chain deformability from the set of normal modes of vibration. This is done by considering each mode as an off‐grid sample of a deformation vector field. Predictions of deformability are compared with experimental data in the form of dihedral angle differences between two conformations of ten kinases by using a modified correlation function. Deformability calculations correlate well with experimental results and validate the applicability of this method to protein flexibility predictions. Proteins 2004. © 2004 Wiley‐Liss, Inc.