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Titolo:
Automated multiple structure alignment and detection of a common substructural motif
Autore:
Leibowitz, N; Fligelman, ZY; Nussinov, R; Wolfson, HJ;
Indirizzi:
NCI, FCRDC, Lab Expt & Computat Biol, SAIC,Intramural Res Support Program,Ft Detrick, MD 21702 USA NCI Ft Detrick MD USA 21702 Res Support Program,Ft Detrick, MD 21702 USA Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Sch Comp Sci, IL-69978 Tel Aviv, Israel Tel Aviv Univ Tel Aviv Israel IL-69978 mp Sci, IL-69978 Tel Aviv, Israel Tel Aviv Univ, Sackler Fac Med, Dept Human Genet & Mol Med, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel Tel Aviv Univ Tel Aviv Israel IL-69978 ol Med, IL-69978 Tel Aviv, Israel
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 3, volume: 43, anno: 2001,
pagine: 235 - 245
SICI:
0887-3585(20010515)43:3<235:AMSAAD>2.0.ZU;2-C
Fonte:
ISI
Lingua:
ENG
Soggetto:
PROTEIN DATA-BANK; MOLECULAR-SURFACE; REPRESENTATION; INTERFACES; CORE;
Keywords:
multiple structural alignment; geometric hashing; invariants; structural core; multiple structural comparison;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
18
Recensione:
Indirizzi per estratti:
Indirizzo: Nussinov, R NCI, FCRDC, Lab Expt & Computat Biol, SAIC,Intramural Res Support Program,Bldg 469,Room 151, Ft Detrick, MD 21702 USA NCI Bldg 469,Room 151 Ft Detrick MD USA 21702 ck, MD 21702 USA
Citazione:
N. Leibowitz et al., "Automated multiple structure alignment and detection of a common substructural motif", PROTEINS, 43(3), 2001, pp. 235-245

Abstract

While a number of approaches have been geared toward multiple sequence alignments, to date there have been very few approaches to multiple structure alignment and detection of a recurring substructural motif. Among these, none performs both multiple structure comparison and motif detection simultaneously. Further, none considers all structures at the same time, rather than initiating from pairwise molecular comparisons. We present such a multiple structural alignment algorithm. Given an ensemble of protein structures, the algorithm automatically finds the largest common substructure (core) ofC, atoms that appears in all the molecules in the ensemble. The detection of the core and the structural alignment are done simultaneously. Additional structural alignments also are obtained and are ranked by the sizes of the substructural motifs, which are present in the entire ensemble. The method is based on the geometric hashing paradigm, As in our previous structuralcomparison algorithms, it compares the structures in an amino acid sequence order-independent way, and hence the resulting alignment is unaffected byinsertions, deletions and protein chain directionality, As such, it can beapplied to protein surfaces, protein-protein interfaces and protein cores to find the optimally, and suboptimally spatially recurring substructural motifs. There is no predefinition of the motif. We describe the algorithm, demonstrating its efficiency. In particular, we present a range of results for several protein ensembles, with different folds and belonging to the same, or to different, families. Since the algorithm treats molecules as collections of points in three-dimensional space, it can also be applied to other molecules, such as RNA, or drugs. (C) 2001 Wiley-Liss, Inc.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 27/11/20 alle ore 12:48:17