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Published online before print April 23, 2008, 10.1110/ps.073402508
Protein Science (2008), 17:977-982. Published by Cold Spring Harbor Laboratory Press. Copyright © 2008 The Protein Society
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Side chain substitution benchmark for peptide/MHC interaction

Bernhard Knapp, Ulrich Omasits, and Wolfgang Schreiner

Unit for Medical Statistics and Informatics, Section for Biomedical Computer Simulation and Bioinformatics, Medical University of Vienna, A-1090 Vienna, Austria

(RECEIVED December 17, 2007; FINAL REVISION February 12, 2008; ACCEPTED February 15, 2008)

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: MHC; benchmark; side chain substitution; side chain placement; RMSD; rotamers


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