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Loop closure via bond scaling and relaxation
Author(s) -
Zheng Qiang,
Rosenfeld Rakefet,
Vajda Sandor,
Delisi Charles
Publication year - 1993
Publication title -
journal of computational chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.907
H-Index - 188
eISSN - 1096-987X
pISSN - 0192-8651
DOI - 10.1002/jcc.540140508
Subject(s) - closure (psychology) , scaling , statistical physics , loop (graph theory) , relaxation (psychology) , bond , chemical physics , materials science , chemistry , mathematics , physics , geometry , combinatorics , economics , psychology , social psychology , market economy , finance
We describe, test, and apply a new computational algorithm for generating protein loop conformations subject to distance and secondary structure constraints. The algorithm is based upon initial scaling and subsequent relaxation of covalent bond lengths. The scaling‐relaxation procedure needs no additional energy terms and can be readily incorporated into existing molecular modeling packages. The algorithm uses an all‐atom energy function from the outset in a straightforward way so that about 60% of the generated loop conformations are free of severe distortions of covalent bond lengths and angles. An extensive application to the major loop conformations of TFIIIA‐type zinc fingers (Zif268 and ADR1) is presented, as well as preliminary calculations on hypervariable loops of two immunoglobulins (MCPC603 and Bence‐Jones). © 1993 John Wiley & Sons, Inc.