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Titolo:
DERIVATION OF RULES FOR COMPARATIVE PROTEIN MODELING FROM A DATABASE OF PROTEIN-STRUCTURE ALIGNMENTS
Autore:
SALI A; OVERINGTON JP;
Indirizzi:
HARVARD UNIV,DEPT CHEM,12 OXFORD ST CAMBRIDGE MA 02138 PFIZER LTD,CENT RES SANDWICH CT13 9NJ KENT ENGLAND
Titolo Testata:
Protein science
fascicolo: 9, volume: 3, anno: 1994,
pagine: 1582 - 1596
SICI:
0961-8368(1994)3:9<1582:DORFCP>2.0.ZU;2-G
Fonte:
ISI
Lingua:
ENG
Soggetto:
ACID SUBSTITUTION TABLES; GLOBULAR-PROTEINS; 3-DIMENSIONAL STRUCTURE; DATA-BANK; HOMOLOGOUS PROTEINS; RELATIONAL DATABASE; SECONDARY STRUCTURE; TERTIARY TEMPLATES; DISULFIDE BRIDGES; ALPHA-HELICES;
Keywords:
COMPARATIVE PROTEIN MODELING; PROTEIN STRUCTURE ALIGNMENTS; PROTEIN STRUCTURE DATABASE;
Tipo documento:
Article
Natura:
Periodico
Settore Disciplinare:
Science Citation Index Expanded
Citazioni:
67
Recensione:
Indirizzi per estratti:
Citazione:
A. Sali e J.P. Overington, "DERIVATION OF RULES FOR COMPARATIVE PROTEIN MODELING FROM A DATABASE OF PROTEIN-STRUCTURE ALIGNMENTS", Protein science, 3(9), 1994, pp. 1582-1596

Abstract

We describe a database of protein structure alignments as well as methods and tools that use this database to improve comparative protein modeling. The current version of the database contains 105 alignments of similar proteins or protein segments. The database comprises 416 entries, 78,495 residues, 1,233 equivalent entry pairs, and 230,396 pairsof equivalent alignment positions. At present, the main application of the database is to improve comparative modeling by satisfaction of spatial restraints implemented in the program MODELLER (Sali A, Blundell TL, 1993, J Mol Biol 234:779-815). To illustrate the usefulness of the database, the restraints on the conformation of a disulfide bridge provided by an equivalent disulfide bridge in a related structure are derived from the alignments; the prediction success of the disulfide dihedral angle classes is increased to approximately 80%, compared to approximately 55% for modeling that relies on the stereochemistry of disulfide bridges alone. The second example of the use of the database is the derivation of the probability density function for comparative modeling of the cis/trans isomerism of the proline residues; the prediction success is increased from 0% to 82.9% for cis-proline and from 93.3% to 96.2% for trans-proline. The database is available via electronic mail.

ASDD Area Sistemi Dipartimentali e Documentali, Università di Bologna, Catalogo delle riviste ed altri periodici
Documento generato il 01/12/20 alle ore 07:31:01