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A structural alignment kernel for protein structures
- Source :
- Bioinformatics, Bioinformatics, Oxford University Press (OUP), 2007, 23 (9), pp.1090-8. ⟨10.1093/bioinformatics/btl642⟩
- Publication Year :
- 2007
- Publisher :
- HAL CCSD, 2007.
-
Abstract
- Motivation: This work aims to develop computational methods to annotate protein structures in an automated fashion. We employ a support vector machine (SVM) classifier to map from a given class of structures to their corresponding structural (SCOP) or functional (Gene Ontology) annotation. In particular, we build upon recent work describing various kernels for protein structures, where a kernel is a similarity function that the classifier uses to compare pairs of structures.Results: We describe a kernel that is derived in a straightforward fashion from an existing structural alignment program, MAMMOTH. We find in our benchmark experiments that this kernel significantly out-performs a variety of other kernels, including several previously described kernels. Furthermore, in both benchmarks, classifying structures using MAMMOTH alone does not work as well as using an SVM with the MAMMOTH kernel.Availability: http://noble.gs.washington.edu/proj/3dkernelContact: noble@gs.washington.edu
- Subjects :
- Statistics and Probability
Computer science
MESH: Sequence Analysis, Protein
MESH: Sequence Homology, Amino Acid
Structural alignment
Molecular Sequence Data
MESH: Sequence Alignment
MESH: Algorithms
MESH: Amino Acid Sequence
Machine learning
computer.software_genre
Biochemistry
Pattern Recognition, Automated
03 medical and health sciences
Kernel (linear algebra)
String kernel
Artificial Intelligence
Sequence Analysis, Protein
MESH: Artificial Intelligence
MESH: Pattern Recognition, Automated
MESH: Proteins
Amino Acid Sequence
Molecular Biology
030304 developmental biology
0303 health sciences
MESH: Molecular Sequence Data
Sequence Homology, Amino Acid
business.industry
030302 biochemistry & molecular biology
Proteins
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Support vector machine
Computational Mathematics
Kernel method
Computational Theory and Mathematics
Radial basis function kernel
Artificial intelligence
Tree kernel
[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]
business
Classifier (UML)
computer
Sequence Alignment
Algorithms
Subjects
Details
- Language :
- English
- ISSN :
- 13674803 and 13674811
- Database :
- OpenAIRE
- Journal :
- Bioinformatics, Bioinformatics, Oxford University Press (OUP), 2007, 23 (9), pp.1090-8. ⟨10.1093/bioinformatics/btl642⟩
- Accession number :
- edsair.doi.dedup.....350ae6af219d32eeb7c9e5489d51fe49