A database method for automated map interpretation in protein crystallography.
Proteins
; 36(4): 526-41, 1999 Sep 01.
Article
en En
| MEDLINE
| ID: mdl-10450094
ABSTRACT
A significant portion of new protein structures contain folds that are related to those seen before. During the development of a computer program that can accurately position, in electron density maps, large protein domains with large structural deviations, it became apparent that the redundancy in protein folds could be used in a non trivial manner during a protein structure determination. As a result a computational procedure, Database Assisted Density Interpretation (DADI), was developed and tested to aid in the building of models in protein crystallography and to assist in interpreting electron density maps. The initial tests of the DADI procedure using a small database of protein domains are described. The philosophy is to first work with entire domains then with the secondary structure elements of these domains and finally with individual residues of the secondary structure elements via Monte Carlo, "chopping" and "clipping" procedures, respectively. The first test case was a traceable 3.2 A multiple isomorphous replacement with anomalous scattering (MIRAS) electron density map of a human topoisomerase I-DNA complex. The second test case uses poor electron density for the third domain of the diphtheria toxin repressor resulting from a molecular replacement solution with the first two domains. Despite the fact that a fairly small database was employed in these test cases, the DADI procedure was able to find a large portion of the protein backbone with very few errors. In the first case nearly 45% of the backbone and more than 80% of the secondary structure was placed automatically. In the second test case nearly 50% of the third domain was automatically detected. A particular encouraging result was that in both cases more than 75% of the beta sheet secondary structure was found automatically by the DADI procedure. Clearly, the procedures employed are promising avenues to exploit the current explosion of protein structures for the determination of future structures. Proteins 1999;36526-541.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Simulación por Computador
/
Proteínas
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Modelos Moleculares
/
Bases de Datos Factuales
/
Cristalografía por Rayos X
Tipo de estudio:
Health_economic_evaluation
Límite:
Animals
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Humans
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
1999
Tipo del documento:
Article
País de afiliación:
Estados Unidos