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Titolo:
Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets
Autore:
Lee, J; Liwo, A; Ripoll, DR; Pillardy, J; Saunders, JA; Gibson, KD; 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 Univ Gdansk, Fac Chem, PL-80952 Gdansk, Poland Univ Gdansk Gdansk PolandPL-80952 sk, Fac Chem, PL-80952 Gdansk, Poland Cornell Theory Ctr, Ithaca, NY 14853 USA Cornell Theory Ctr Ithaca NY USA14853 l Theory Ctr, Ithaca, NY 14853 USA
Titolo Testata:
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
fascicolo: 1, volume: 77, anno: 2000,
pagine: 90 - 117
SICI:
0020-7608(20000305)77:1<90:HEATPP>2.0.ZU;2-D
Fonte:
ISI
Lingua:
ENG
Soggetto:
MULTIPLE-MINIMA PROBLEM; DRIVEN MONTE-CARLO; PANCREATIC TRYPSIN-INHIBITOR; DIFFUSION EQUATION METHOD; RESIDUE FORCE-FIELD; HYDROGEN-BOND INTERACTIONS; MEMBRANE-BOUND PORTION; OCCURRING AMINO-ACIDS; CONFORMATIONAL-ANALYSIS; NONBONDED INTERACTIONS;
Keywords:
protein folding; global optimization; conformational search; potential energy function; structure prediction;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Physical, Chemical & Earth Sciences
Citazioni:
95
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., "Hierarchical energy-based approach to protein-structure prediction: Blind-test evaluation with CASP3 targets", INT J QUANT, 77(1), 2000, pp. 90-117

Abstract

A hierarchical approach based exclusively on finding the global minimum ofan appropriate potential energy function, without the aid of secondary structure prediction, multiple-sequence alignment, or threading, is proposed. The procedure starts from an extensive search of the conformational space of a protein, using our recently developed united-residue off-lattice UNRES force field and the conformational space annealing (CSA) method. The structures obtained in the search are clustered into families and ranked according to their UNRES energy Structures within a preassigned energy cutoff are gradually converted into an all-atom representation, followed by a limited conformational search at the all-atom level, using the electrostatically driven Monte Carlo (EDMC) method and the ECEPP/3 force field including hydration. The approach was tested (in the CASP3 experiment) in blind predictions on seven targets, five of which were globular proteins with sizes ranging from 89 to 140 amino acid residues. Comparison of the computed lowest-energystructures, with the experimental structures, made available after the predictions were submitted, shows that large fragments (similar to 60 residues, representing 45-80% of the proteins) of those five globular proteins werepredicted with the root mean square deviations (RMSDs) ranging from 4 to 7Angstrom for the C-alpha atoms, with correct secondary structure and topology. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence. (C) 2000 John Wiley & Sons, Inc.

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Documento generato il 14/07/20 alle ore 02:33:50