Prediction of Protein Binding Sites in Protein Structures Using Hidden Markov Support Vector Machine

Slate:the target protein. Blue:the binding partner. Magenta:interface residues. SSSEIKIVRDEYGMPHIYANDTWHLFYGYG IIINIINNIINNNIIIIIIINIINIIINNN Input Output

Machine Learning Methods Applied Classification methods Sequential labelling methods ANNSVM CRF

FEATURES Neighboring residue profile feature Neighboring residue profile feature Hydrophobicity Hydrophobicity Sequence conservation Sequence conservation Secondary structure Secondary structure Solvent accessible surface area Solvent accessible surface area

Hidden Markov Support Vector Machine Emission feature function Transition feature function Corresponding weight

Hidden Markov Support Vector Machine  Spatially neighboring residue profile feature  Spatially neighboring residue accessible surface (ASA) feature Emission feature function

Hidden Markov Support Vector Machine Transition feature function

Hidden Markov Support Vector Machine Transition feature function

Hidden Markov Support Vector Machine Corresponding weight

Hidden Markov Support Vector Machine Source Code: ☆ The cutting-plane algorithm makes it linear

DATA SET

Influence of the number of training samples on the prediction performance and running time

The inter-relation information between neighboring residues is relevant for discrimination

The window size has not significant influence on the performance

Actual interface residues ANN SVMCRFHM-SVM Comparison with related methods

Actual interface residues ANN SVMCRFHM-SVM Comparison with related methods

SUMMARY Prediction of protein binding sites Prediction of protein binding sites Hidden Markov Support Vector Machine Hidden Markov Support Vector Machine Result Analysis Result Analysis Comparison with other methods Comparison with other methods Influence of the number of training samples Influence of the number of training samples The information between neighboring residues The information between neighboring residues Window size Window size Discussion Discussion