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Titolo:
Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories
Autore:
Kedem, K; Chew, LP; Elber, R;
Indirizzi:
Cornell Univ, Dept Comp Sci, Ithaca, NY 14853 USA Cornell Univ Ithaca NY USA 14853 niv, Dept Comp Sci, Ithaca, NY 14853 USA
Titolo Testata:
PROTEINS-STRUCTURE FUNCTION AND GENETICS
fascicolo: 4, volume: 37, anno: 1999,
pagine: 554 - 564
SICI:
0887-3585(199912)37:4<554:UR(AAT>2.0.ZU;2-O
Fonte:
ISI
Lingua:
ENG
Soggetto:
PROTEINS;
Keywords:
root mean square distance; structure comparison; folding; C peptide; order parameter;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Life Sciences
Citazioni:
21
Recensione:
Indirizzi per estratti:
Indirizzo: Elber, R Cornell Univ, Dept Comp Sci, 4130 Upsom Hall, Ithaca, NY 14853 USA Cornell Univ 4130 Upsom Hall Ithaca NY USA 14853 ca, NY 14853 USA
Citazione:
K. Kedem et al., "Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories", PROTEINS, 37(4), 1999, pp. 554-564

Abstract

The Unit-vector RMS (URMS) is a new technique to compare protein chains and to detect similarities of chain segments. It is limited to comparison of C-alpha chains. However, it has a number of unique features that include exceptionally weak dependence on the length of the chain and efficient detection of substructure similarities. Two molecular dynamics simulations of proteins in the neighborhood of their native states are used to test the performance of the URMS. The first simulation is of a solvated myoglobin and thesecond is of the protein MHC, In accord with previous studies the secondary structure elements (helices or sheets) are found to be moving relatively rigidly among flexible loops, In addition to these tests, folding trajectories of C peptides are analyzed, revealing a folding nucleus of seven amino acids, Proteins 1999;37: 554-564, (C) 1999Wiley-Liss, Inc.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 06/07/20 alle ore 04:23:50