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Titolo:
Learning effective amino acid interactions through iterative stochastic techniques
Autore:
Micheletti, C; Seno, F; Banavar, JR; Maritan, A;
Indirizzi:
Int Sch Adv Studies, I-34014 Trieste, Italy Int Sch Adv Studies Trieste Italy I-34014 tudies, I-34014 Trieste, Italy INFM, I-34014 Trieste, Italy INFM Trieste Italy I-34014INFM, I-34014 Trieste, Italy INFM, Dipartimento G Galilei, Padua, Italy INFM Padua ItalyINFM, Dipartimento G Galilei, Padua, Italy Penn State Univ, Davey Lab 104, University Pk, PA 16802 USA Penn State Univ University Pk PA USA 16802 4, University Pk, PA 16802 USA
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 3, volume: 42, anno: 2001,
pagine: 422 - 431
SICI:
0887-3585(20010215)42:3<422:LEAAIT>2.0.ZU;2-1
Fonte:
ISI
Lingua:
ENG
Soggetto:
PROTEIN STRUCTURES; INTERACTION POTENTIALS; GLOBULAR-PROTEINS; DESIGN; PREDICTION; MODELS; RECOGNITION; ACCURACY; SPACES; FORCE;
Keywords:
protein folding; knowledge-based potential extraction; optimization of thermodynamic stability; effective scoring functions; iterative stochastic techniques; Monte Carlo dynamics;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
47
Recensione:
Indirizzi per estratti:
Indirizzo: Micheletti, C Int Sch Adv Studies, Via Beirut 2, I-34014 Trieste, Italy Int Sch Adv Studies Via Beirut 2 Trieste Italy I-34014 taly
Citazione:
C. Micheletti et al., "Learning effective amino acid interactions through iterative stochastic techniques", PROTEINS, 42(3), 2001, pp. 422-431

Abstract

The prediction of the three-dimensional structures of the native states ofproteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essen tial task for solving this problem within coarse-grained models is the deduction of effective interaction potentials between the amino acids. Over the years, several techniques have been developed to extract potentials that are able to discriminate satisfactorily between the native and nonnative folds of a preassigned protein sequence. In general, when these potentials are used in actual dynamical folding simulations, they lead to a drift of the native structure outside the quasinative basin. In this article, we present and validate an approach to overcome this difficulty. By exploiting several numerical and analytical tools, we set up a rigorous iterative scheme to extract potentials satisfyinga prerequisite of any viable potential: the stabilization of proteins within their native basin (less than 3-4 Angstrom RMSD). The scheme is flexibleand is demonstrated to be applicable to a variety of parameterizations of the energy function, and it provides in each case the optimal potentials. Proteins 2001;42:422-431. (C) 2001 Wiley-Liss, Inc.

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Documento generato il 07/07/20 alle ore 15:40:57