Format

Send to

Choose Destination
Curr Protein Pept Sci. 2008 Feb;9(1):70-95.

Homology-free prediction of functional class of proteins and peptides by support vector machines.

Author information

1
Bioinformatics and Drug Design Group, Department of Pharmacy and Center for Computational Science and Engineering, National University of Singapore, Blk S16, Level 8, 3 Science Drive 2, Singapore.

Abstract

Protein and peptide sequences contain clues for functional prediction. A challenge is to predict sequences that show low or no homology to proteins or peptides of known function. A machine learning method, support vector machines (SVM), has recently been explored for predicting functional class of proteins and peptides from sequence-derived properties irrespective of sequence similarity, which has shown impressive performance for predicting a wide range of protein and peptide classes including certain low- and non- homologous sequences. This method serves as a new and valuable addition to complement the extensively-used alignment-based, clustering-based, and structure-based functional prediction methods. This article evaluates the strategies, current progresses, reported prediction performances, available software tools, and underlying difficulties in using SVM for predicting the functional class of proteins and peptides.

PMID:
18336324
[Indexed for MEDLINE]

Supplemental Content

Full text links

Icon for Bentham Science Publishers Ltd.
Loading ...
Support Center