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Titolo:
Conformation-Family Monte Carlo (CFMC): An efficient computational method for identifying the low-energy states of a macromolecule
Autore:
Pillardy, J; Czaplewski, C; 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
Titolo Testata:
HELVETICA CHIMICA ACTA
fascicolo: 9, volume: 83, anno: 2000,
pagine: 2214 - 2230
SICI:
0018-019X(2000)83:9<2214:CMC(AE>2.0.ZU;2-X
Fonte:
ISI
Lingua:
ENG
Soggetto:
RESIDUE FORCE-FIELD; PROTEIN-STRUCTURE SIMULATIONS; MULTIPLE-MINIMA PROBLEM; GLOBAL OPTIMIZATION METHOD; LENNARD-JONES ATOMS; NONBONDED INTERACTIONS; APPROXIMATE SOLUTION; OPTIMUM STRUCTURES; POLYPEPTIDES; CLUSTERS;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Physical, Chemical & Earth Sciences
Citazioni:
36
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. Pillardy et al., "Conformation-Family Monte Carlo (CFMC): An efficient computational method for identifying the low-energy states of a macromolecule", HELV CHIM A, 83(9), 2000, pp. 2214-2230

Abstract

A highly efficient method, Conformation-Family Monte Carlo (CFMC), has been developed for searching the conformational space of a macromolecule and identifying its low-energy conformations. This method maintains a database of low-energy conformations that are clustered into families. The conformations in this database are improved iteratively by a Metropolis-type Monte Carlo procedure, together with energy minimization, in which the search is biased towards investigating the regions of the lowest-energy families. The CFMC method has the advantages of our earlier potential-smoothing methods tin that it 'coarse-grains' the conformational space and exploits informationabout nearby low-energy states), but avoids their disadvantages (such as the displacement of the global minimum at large smoothings). The CFMC methodis applied to a test protein, domain B of Staphylococcal protein A. Independent CFMC runs yielded the same low-energy families of conformations from random starts indicating that the thermodynamically relevant conformationalspace of this protein has been explored thoroughly. The CFMC method is highly efficient, performing as well as or better than competing methods, suchas Monte Carlo with minimization, conformational-space annealing, and the self-consistent basin-to-deformed-basin method.

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Documento generato il 24/09/20 alle ore 05:03:56