Discrimination of outer membrane proteins using support vector machines.
BACKGROUND
Discriminating outer membrane proteins from other folding types of globular and membrane proteins is an important task both for dissecting outer membrane proteins (OMPs) from genomic sequences and for the successful prediction of their secondary and tertiary structures.


RESULTS
We have developed a method based on support vector machines using amino acid composition and residue pair information. Our approach with amino acid composition has correctly predicted the OMPs with a cross-validated accuracy of 94% in a set of 208 proteins. Further, this method has successfully excluded 633 of 673 globular proteins and 191 of 206 alpha-helical membrane proteins. We obtained an overall accuracy of 92% for correctly picking up the OMPs from a dataset of 1087 proteins belonging to all different types of globular and membrane proteins. Furthermore, residue pair information improved the accuracy from 92 to 94%. This accuracy of discriminating OMPs is higher than that of other methods in the literature, which could be used for dissecting OMPs from genomic sequences.


BACKGROUND
Discrimination results are available at http://tmbeta-svm.cbrc.jp.
Park
Keun-Joon
KJ
Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Koto-ku, Tokyo 135-0064, Japan.
Gromiha
M Michael
MM
Horton
Paul
P
Suwa
Makiko
M
D000465:Algorithms; D001185:Artificial Intelligence; D001425:Bacterial Outer Membrane Proteins / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005822:Genetic Vectors; D016678:Genome; D006801:Humans; D020407:Internet; D008565:Membrane Proteins / Q000737:chemistry; D015233:Models, Statistical; D010363:Pattern Recognition, Automated; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
D001425:Bacterial Outer Membrane Proteins; D008565:Membrane Proteins