Side chain substitution benchmark for peptide/MHC interaction.

Protein Science : a Publication of the Protein Society
Bernhard KnappWolfgang Schreiner

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.

References

Jul 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·C GrégoireB Malissen
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Adrian A CanutescuRoland L Dunbrack
Jun 25, 2004·Nucleic Acids Research·R GautierP Tufféry
Apr 21, 2005·Protein Science : a Publication of the Protein Society·Björn Wallner, Arne Elofsson
Feb 1, 2006·Proteins·Huynh-Hoa BuiIan S Haworth
Mar 23, 2006·Annual Review of Immunology·Markus G RudolphIan A Wilson
Nov 2, 2006·Briefings in Bioinformatics·Joo Chuan TongShoba Ranganathan
Jun 15, 2007·Protein Science : a Publication of the Protein Society·Christoph HartmannThomas Lengauer

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Citations

Feb 6, 2009·Journal of Computer-aided Molecular Design·Bernhard KnappWolfgang Schreiner
Oct 12, 2010·Journal of Computer-aided Molecular Design·Constanza CárdenasF Javier Luque
Jun 18, 2011·BMC Bioinformatics·Bernhard KnappWolfgang Schreiner
Jul 26, 2012·Bioinformation·Mahesh ShrinivasanVinod Rama Kolte
Sep 29, 2012·Computational and Mathematical Methods in Medicine·Wolfgang SchreinerNevena Ilieva
Dec 4, 2015·Journal of Chemical Information and Modeling·Bernhard Knapp, Charlotte M Deane
Mar 1, 2015·Briefings in Bioinformatics·Bernhard KnappCharlotte M Deane
Oct 26, 2018·Journal of Chemical Theory and Computation·Bernhard KnappCharlotte M Deane

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