Prediction of protein-protein interactions between viruses and human by an SVM model.
BMC Bioinformatics
; 13 Suppl 7: S5, 2012 May 08.
Article
en En
| MEDLINE
| ID: mdl-22595002
ABSTRACT
BACKGROUND:
Several computational methods have been developed to predict protein-protein interactions from amino acid sequences, but most of those methods are intended for the interactions within a species rather than for interactions across different species. Methods for predicting interactions between homogeneous proteins are not appropriate for finding those between heterogeneous proteins since they do not distinguish the interactions between proteins of the same species from those of different species.RESULTS:
We developed a new method for representing a protein sequence of variable length in a frequency vector of fixed length, which encodes the relative frequency of three consecutive amino acids of a sequence. We built a support vector machine (SVM) model to predict human proteins that interact with virus proteins. In two types of viruses, human papillomaviruses (HPV) and hepatitis C virus (HCV), our SVM model achieved an average accuracy above 80%, which is higher than that of another SVM model with a different representation scheme. Using the SVM model and Gene Ontology (GO) annotations of proteins, we predicted new interactions between virus proteins and human proteins.CONCLUSIONS:
Encoding the relative frequency of amino acid triplets of a protein sequence is a simple yet powerful representation method for predicting protein-protein interactions across different species. The representation method has several advantages (1) it enables a prediction model to achieve a better performance than other representations, (2) it generates feature vectors of fixed length regardless of the sequence length, and (3) the same representation is applicable to different types of proteins.
Texto completo:
1
Banco de datos:
MEDLINE
Asunto principal:
Papillomaviridae
/
Proteínas
/
Hepacivirus
/
Interacciones Huésped-Patógeno
/
Máquina de Vectores de Soporte
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Límite:
Humans
Idioma:
En
Revista:
BMC Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2012
Tipo del documento:
Article
País de afiliación:
Corea del Sur