Evaluation of threading specificity and accuracy.
Proteins
; 26(2): 172-85, 1996 Oct.
Article
en En
| MEDLINE
| ID: mdl-8916225
Threading experiments with proteins from the globin family provide an indication of the nature of the structural similarity required for successful fold recognition and accurate sequence-structure alignment. Threading scores are found to rise above the noise of false positives whenever roughly 60% of residues from a sequence can be aligned with analogous sites in the structure of a remote homolog. Fold recognition specificity thus appears to be limited by the extent of structural similarity, regardless of the degree of sequence similarity. Threading alignment accuracy is found to depend more critically on the degree of structural similarity. Alignments are accurate, placing the majority of residues exactly as in structural alignment, only when superposition residuals are less than 2.5 A. These criteria for successful recognition and sequence-structure alignment appear to be consistent with the successes and failures of threading methods in blind structure prediction. They also suggest a direct assay for improved threading methods: Potentials and alignment models should be tested for their ability to detect less extensive structural similarities, and to produce accurate alignments when superposition residuals for this conserved "core" fall in the range characteristic of remote homologs.
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Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Pliegue de Proteína
Tipo de estudio:
Diagnostic_studies
/
Evaluation_studies
/
Prognostic_studies
Idioma:
En
Revista:
Proteins
Asunto de la revista:
BIOQUIMICA
Año:
1996
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Estados Unidos