Support vector machines for prediction of dihedral angle regions

• Published in: Bioinformatics Vol. 22; no. 24; pp. 3009 - 3015
• Main Authors: Zimmermann, Olav, Hansmann, Ulrich H. E.
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-12-2006; Oxford Publishing Limited (England)
• Subjects: Algorithms; Amino Acid Sequence; Artificial Intelligence; Biological and medical sciences; Computer Simulation; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Chemical; Models, Molecular; Molecular Sequence Data; Pattern Recognition, Automated - methods; Protein Structure, Secondary; Proteins - chemistry; Proteins - ultrastructure; Sequence Alignment - methods; Sequence Analysis, Protein - methods; Order; Prediction; Web service; Support vector machine; Secondary structure; Premises; Original document; Angle; Aminoacid; Region; Dihedron; Random coil; Bioinformatics
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btl489

Motivation: Most secondary structure prediction programs target only alpha helix and beta sheet structures and summarize all other structures in the random coil pseudo class. However, such an assignment often ignores existing local ordering in so-called random coil regions. Signatures for such ordering are distinct dihedral angle pattern. For this reason, we propose as an alternative approach to predict directly dihedral regions for each residue as this leads to a higher amount of structural information. Results: We propose a multi-step support vector machine (SVM) procedure, dihedral prediction (DHPRED), to predict the dihedral angle state of residues from sequence. Trained on 20 000 residues our approach leads to dihedral region predictions, that in regions without alpha helices or beta sheets is higher than those from secondary structure prediction programs. Availability: DHPRED has been implemented as a web service, which academic researchers can access from our webpage Contact:[e-mail]