Pcleavage: an SVM based method for prediction of constitutive proteasome and immunoproteasome cleavage sites in antigenic sequences
Open Access
- 1 July 2005
- journal article
- research article
- Published by Oxford University Press (OUP) in Nucleic Acids Research
- Vol. 33 (Web Server) , W202-W207
- https://doi.org/10.1093/nar/gki587
Abstract
This manuscript describes a support vector machine based method for the prediction of constitutive as well as immunoproteasome cleavage sites in antigenic sequences. This method achieved Matthew's correlation coefficents of 0.54 and 0.43 on in vitro and major histocompatibility complex ligand data, respectively. This shows that the performance of our method is comparable to that of the NetChop method, which is currently considered to be the best method for proteasome cleavage site prediction. Based on the method, a web server, Pcleavage, has also been developed. This server accepts protein sequences in any standard format and present results in a user-friendly format. The server is available for free use by all academic users at the URL http://www.imtech.res.in/raghava/pcleavage/ or http://bioinformatics.uams.edu/mirror/pcleavage/.Keywords
This publication has 12 references indexed in Scilit:
- Predicting proteasomal cleavage sites: a comparison of available methodsInternational Immunology, 2003
- Discrete Cleavage Motifs of Constitutive and Immunoproteasomes Revealed by Quantitative Analysis of Cleavage ProductsThe Journal of Experimental Medicine, 2001
- PAProC: a prediction algorithm for proteasomal cleavages available on the WWWImmunogenetics, 2001
- The Human 26 S and 20 S Proteasomes Generate Overlapping but Different Sets of Peptide Fragments from a Model Protein SubstrateJournal of Biological Chemistry, 2000
- An algorithm for the prediction of proteasomal cleavagesJournal of Molecular Biology, 2000
- Sequence signals for generation of antigenic peptides by the proteasome: implications for proteasomal cleavage mechanismJournal of Molecular Biology, 2000
- DEGRADATION OF CELL PROTEINS AND THE GENERATION OF MHC CLASS I-PRESENTED PEPTIDESAnnual Review of Immunology, 1999
- Specificity of the proteasome and the TAP transporterCurrent Opinion in Immunology, 1999
- A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20s proteasomeJournal of Molecular Biology, 1999
- Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptideProceedings of the National Academy of Sciences, 1997