Combination of threading potentials and sequence profiles improves fold recognition.
J Mol Biol
; 296(5): 1319-31, 2000 Mar 10.
Article
en En
| MEDLINE
| ID: mdl-10698636
Using a benchmark set of structurally similar proteins, we conduct a series of threading experiments intended to identify a scoring function with an optimal combination of contact-potential and sequence-profile terms. The benchmark set is selected to include many medium-difficulty fold recognition targets, where sequence similarity is undetectable by BLAST but structural similarity is extensive. The contact potential is based on the log-odds of non-local contacts involving different amino acid pairs, in native as opposed to randomly compacted structures. The sequence profile term is that used in PSI-BLAST. We find that combination of these terms significantly improves the success rate of fold recognition over use of either term alone, with respect to both recognition sensitivity and the accuracy of threading models. Improvement is greatest for targets between 10 % and 20 % sequence identity and 60 % to 80 % superimposable residues, where the number of models crossing critical accuracy and significance thresholds more than doubles. We suggest that these improvements account for the successful performance of the combined scoring function at CASP3. We discuss possible explanations as to why sequence-profile and contact-potential terms appear complementary.
Buscar en Google
Colección:
01-internacional
Base de datos:
MEDLINE
Asunto principal:
Algoritmos
/
Proteínas
/
Alineación de Secuencia
/
Homología de Secuencia de Aminoácido
/
Pliegue de Proteína
/
Biología Computacional
Tipo de estudio:
Diagnostic_studies
/
Prognostic_studies
Idioma:
En
Revista:
J Mol Biol
Año:
2000
Tipo del documento:
Article
País de afiliación:
Estados Unidos
Pais de publicación:
Países Bajos