Large-scale validation of methods for cytotoxic T-lymphocyte epitope prediction
Top Cited Papers
Open Access
- 31 October 2007
- journal article
- research article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 8 (1) , 424
- https://doi.org/10.1186/1471-2105-8-424
Abstract
Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web-based tool designed for predicting human CTL epitopes in any given protein. It does so by integrating predictions of proteasomal cleavage, TAP transport efficiency, and MHC class I affinity. At least four other methods have been developed recently that likewise attempt to predict CTL epitopes: EpiJen, MAPPP, MHC-pathway, and WAPP. In order to compare the performance of prediction methods, objective benchmarks and standardized performance measures are needed. Here, we develop such large-scale benchmark and corresponding performance measures and report the performance of an updated version 1.2 of NetCTL in comparison with the four other methods.Keywords
This publication has 32 references indexed in Scilit:
- A Community Resource Benchmarking Predictions of Peptide Binding to MHC-I MoleculesPLoS Computational Biology, 2006
- Functional Dissection of the Transmembrane Domains of the Transporter Associated with Antigen Processing (TAP)Journal of Biological Chemistry, 2004
- Reliable prediction of T‐cell epitopes using neural networks with novel sequence representationsProtein Science, 2003
- 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
- IMMUNODOMINANCE IN MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I–RESTRICTED T LYMPHOCYTE RESPONSESAnnual Review of Immunology, 1999
- A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20s proteasomeJournal of Molecular Biology, 1999
- A sequential model for peptide binding and transport by the transporters associated with antigen processingImmunity, 1994
- HLA-A2 molecules in an antigen-processing mutant cell contain signal sequence-derived peptidesNature, 1992
- HLA-A2.1-Associated Peptides from a Mutant Cell Line: A Second Pathway of Antigen PresentationScience, 1992