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Titolo:
Optimization of parameters in macromolecular potential energy functions byconformational space annealing
Autore:
Lee, J; Ripoll, DR; Czaplewski, C; Pillardy, J; Wedemeyer, WJ; Scheraga, HA;
Indirizzi:
Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 b Chem & Chem Biol, Ithaca, NY 14853 USA Korea Inst Adv Study, Program Computat Sci, Seoul 130012, South Korea Korea Inst Adv Study Seoul South Korea 130012 Seoul 130012, South Korea Cornell Theory Ctr, Ithaca, NY 14853 USA Cornell Theory Ctr Ithaca NY USA14853 l Theory Ctr, Ithaca, NY 14853 USA Univ Gdansk, Fac Chem, PL-80952 Gdansk, Poland Univ Gdansk Gdansk PolandPL-80952 sk, Fac Chem, PL-80952 Gdansk, Poland
Titolo Testata:
JOURNAL OF PHYSICAL CHEMISTRY B
fascicolo: 30, volume: 105, anno: 2001,
pagine: 7291 - 7298
SICI:
1520-6106(20010802)105:30<7291:OOPIMP>2.0.ZU;2-2
Fonte:
ISI
Lingua:
ENG
Soggetto:
RESIDUE FORCE-FIELD; PROTEIN-STRUCTURE SIMULATIONS; HYDROGEN-BOND INTERACTIONS; MEMBRANE-BOUND PORTION; OCCURRING AMINO-ACIDS; NONBONDED INTERACTIONS; GEOMETRICAL PARAMETERS; STRUCTURE PREDICTION; GLOBULAR-PROTEINS; Z-SCORE;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
35
Recensione:
Indirizzi per estratti:
Indirizzo: Scheraga, HA Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 Biol, Ithaca, NY 14853 USA
Citazione:
J. Lee et al., "Optimization of parameters in macromolecular potential energy functions byconformational space annealing", J PHYS CH B, 105(30), 2001, pp. 7291-7298

Abstract

A general protocol for refining the parameters of macromolecular potentialenergy functions by optimizing criteria that compare nativelike and normative conformations of one or more benchmark protein(s) is described. The protocol exploits the high efficiency of conformational space annealing (CSA) in finding the lowest-energy conformation of an isolated macromolecule. A novel form of the CSA method, local CSA, is introduced to provide better sampling of nativelike conformations. The computational expense of the protocol is reduced significantly by a linear approximation that estimates the energy of the (reminimized) native and normative conformations after every change of the force field parameters. The protocol is illustrated by optimizing the parameters of two force fields used in the CASP3 and CASP4 experiments, respectively. Another version of this general protocol (with different optimization criteria and optimization methods) was used to determine the parameters for the alpha, beta and alpha/beta force fields used in the CASP4 experiment, as reported in a companion publication.

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Documento generato il 08/07/20 alle ore 07:49:08