Side chain substitution benchmark for peptide/MHC interaction
- 1 June 2008
- journal article
- Published by Wiley in Protein Science
- Vol. 17 (6) , 977-982
- https://doi.org/10.1110/ps.073402508
Abstract
The prediction of T-cell epitopes is an essential part in virtual immunology. Apart from sequence-based techniques, which achieve good results but fail to give insight into the binding behavior of a certain peptide binding to a major histocompatibility complex, structure-based approaches are another important technique. An essential step is the correct placement of the side chains for a given peptide in cases where no experimental data for the structure are available. To our knowledge, no benchmark for side chain substitution in the area of HLA has been reported in the literature. Here, we present a comparison of five different tools (SCWRL, SCATD, SPDBV, SCit, IRECS) applicable for side chain substitution. Each tool is tested on 29 different HLA-A2 structures with experimentally known side chain positions. Parts of the benchmark are correctness, reliability, runtime, and usability. For validation, the root mean square deviations between X-ray structures and predicted structures are used. All tools show different strengths and weaknesses.Keywords
This publication has 17 references indexed in Scilit:
- IRECS: A new algorithm for the selection of most probable ensembles of side‐chain conformations in protein modelsProtein Science, 2007
- Ab initio prediction of peptide‐MHC binding geometry for diverse class I MHC allotypesProteins-Structure Function and Bioinformatics, 2006
- Structural prediction of peptides binding to MHC class I moleculesProteins-Structure Function and Bioinformatics, 2006
- SCit: web tools for protein side chain conformation analysisNucleic Acids Research, 2004
- A graph‐theory algorithm for rapid protein side‐chain predictionProtein Science, 2003
- The Protein Data BankNucleic Acids Research, 2000
- SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modelingElectrophoresis, 1997
- Covalent assembly of a soluble T cell receptor-peptide-major histocompatibility class I complex.Proceedings of the National Academy of Sciences, 1996
- GROMACS: A message-passing parallel molecular dynamics implementationComputer Physics Communications, 1995
- The three-dimensional structure of HLA-B27 at 2.1 Å resolution suggests a general mechanism for tight peptide binding to MHCCell, 1992