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The reconstruction of a protein backbone from C α coordinates
Author(s) -
Gan Kaiwan,
Alexander Peter,
Coxon James M.,
McKin A. John,
Worth Gillian H.
Publication year - 1997
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/(sici)1097-0282(19970405)41:4<381::aid-bip3>3.0.co;2-i
Subject(s) - dihedral angle , chemistry , force field (fiction) , absolute deviation , energy minimization , base (topology) , standard deviation , monte carlo method , crystallography , computational chemistry , geometry , molecule , statistics , mathematical analysis , mathematics , artificial intelligence , computer science , hydrogen bond , organic chemistry
A Monte Carlo Protein Building method to construct the backbone and C β atomic coordinates from known C α coordinates is reported. The method selects values of dihedral angles from ranges established from a statistical analysis of the relationship between dihedral angles of the backbone and C α coordinates for a protein data base. The averaged coordinates from ten backbone models of a protein were used to define a mean structure that was refined by energy minimization using the AMBER force field (GB/SA). By the latter method the average atomic deviation and rmsd of the backbone and C β atoms for 24 proteins is between 0.14 and 0.32 Å (average 0.22 Å) and 0.22 and 0.61 Å (average 0.43 Å), respectively. A comparison with other methods is made. © 1997 John Wiley & Sons, Inc.