TIM-Finder: a new method for identifying TIM-barrel proteins.
BMC Struct Biol
; 9: 73, 2009 Dec 14.
Article
en En
| MEDLINE
| ID: mdl-20003393
ABSTRACT
BACKGROUND:
The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required.RESULTS:
To develop a new TIM-barrel protein identification method in this work, we consider three descriptors a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method.CONCLUSIONS:
TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http//202.112.170.199/TIM-Finder/.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Bacillus subtilis
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Triosa-Fosfato Isomerasa
/
Pliegue de Proteína
/
Biología Computacional
/
Proteoma
Tipo de estudio:
Prognostic_studies
Idioma:
En
Revista:
BMC Struct Biol
Asunto de la revista:
BIOLOGIA
Año:
2009
Tipo del documento:
Article
País de afiliación:
China