Influence of amino acid properties for discriminating outer membrane proteins at better accuracy.
Discriminating outer membrane proteins (OMPs) from other folding types of globular and membrane proteins is an important task both for identifying outer membrane proteins from genomic sequences and for the successful prediction of their secondary and tertiary structures. In this work, we have analyzed the influence of physico-chemical, energetic and conformational properties of amino acid residues for discriminating outer membrane proteins using different machine learning algorithms, such as, Bayes rules, Logistic functions, Neural networks, Support vector machines, Decision trees, etc. We observed that most of the properties have discriminated the OMPs with similar accuracy. The neural network method with the property, free energy change could discriminate the OMPs from other folding types of globular and membrane proteins at the 5-fold cross-validation accuracy of 94.4% in a dataset of 1,088 proteins, which is better than that obtained with amino acid composition. The accuracy of discriminating globular proteins is 94.3% and that of transmembrane helical (TMH) proteins is 91.8%. Further, the neural network method is tested with globular proteins belonging to 30 major folding types and it could successfully exclude 99.4% of the considered 1612 non-redundant proteins. These accuracy levels are comparable to or better than other methods in the literature. We suggest that this method could be effectively used to discriminate OMPs and for detecting OMPs in genomic sequences.
Gromiha
M Michael
MM
Computational Biology Research Center, CBRC, National Institute of Advanced Industrial Science and Technology, AIST Tokyo Waterfront Bio-IT Research Building, 2-42 Aomi, Tokyo 135-0064, Japan. michael-gromiha@aist.go.jp
Suwa
Makiko
M
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry*; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry*; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D008968:Molecular Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012680:Sensitivity and Specificity; D013816:Thermodynamics
D000596:Amino Acids; D001425:Bacterial Outer Membrane Proteins