CASVM: web server for SVM-based prediction of caspase substrates cleavage sites
| Autor: | Lawrence J K Wee, Tin Wee Tan, Shoba Ranganathan |
|---|---|
| Rok vydání: | 2007 |
| Předmět: |
Statistics and Probability
Web server Proteases Sequence analysis Computer science Molecular Sequence Data information science Computational biology computer.software_genre Cleavage (embryo) Biochemistry Pattern Recognition Automated Substrate Specificity Artificial Intelligence Sequence Analysis Protein Protein methods Amino Acid Sequence Binding site Molecular Biology Peptide sequence Caspase computer.programming_language chemistry.chemical_classification Internet Binding Sites biology Tetrapeptide Computer Science Applications Enzyme Activation Computational Mathematics Enzyme Computational Theory and Mathematics chemistry Apoptosis Caspases biology.protein Data mining Perl Aspartic acid residue Sequence Alignment computer Algorithms Software Protein Binding Cysteine |
| Zdroj: | Bioinformatics. 23:3241-3243 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Summary: Caspases belong to a unique class of cysteine proteases which function as critical effectors of apoptosis, inflammation and other important cellular processes. Caspases cleave substrates at specific tetrapeptide sites after a highly conserved aspartic acid residue. Prediction of such cleavage sites will complement structural and functional studies on substrates cleavage as well as discovery of new substrates. We have recently developed a support vector machines (SVM) method to address this issue. Our algorithm achieved an accuracy ranging from 81.25 to 97.92%, making it one of the best methods currently available. CASVM is the web server implementation of our SVM algorithms, written in Perl and hosted on a Linux platform. The server can be used for predicting non-canonical caspase substrate cleavage sites. We have also included a relational database containing experimentally verified caspase substrates retrievable using accession IDs, keywords or sequence similarity.Availability: http://www.casbase.org/casvm/index.htmlContact: shoba.ranganathan@mq.edu.auSupplementary information: http://www.casbase.org/casvm/help/index.html |
| Databáze: | OpenAIRE |
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