| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
1 Department of Biochemistry, National University of Singapore, Singapore 119260
2 Research Institute for Biotechnology, Macquarie University, NSW 2109, Australia
(RECEIVED January 12, 2004; FINAL REVISION April 16, 2004; ACCEPTED May 27, 2004)
In this article, we present a new technique for the rapid and precise docking of peptides to MHC class I and class II receptors. Our docking procedure consists of three steps: (1) peptide residues near the ends of the binding groove are docked by using an efficient pseudo-Brownian rigid body docking procedure followed by (2) loop closure of the intervening backbone structure by satisfaction of spatial constraints, and subsequently, (3) the refinement of the entire backbone and ligand interacting side chains and receptor side chains experiencing atomic clash at the MHC receptor–peptide interface. The method was tested by remodeling of 40 nonredundant complexes of at least 3.00 Å resolution for which three-dimensional structural information is available and independently for docking peptides derived from 15 nonredundant complexes into a single template structure. In the first test, 33 out of 40 MHC class I and class II peptides and in the second test, 11 out of 15 MHC–peptide complexes were modeled with a C
RMSD < 1.00 Å.
Keywords: major histocompatibility complex; epitope prediction; flexible docking; immunology; Monte Carlo
Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04631204.
Reprint requests to: Shoba Ranganathan, MU Biotechnology Research Institute, Building F7B-233, Macquarie University, NSW 2109, Australia; e-mail: shoba.ranganathan{at}mq.edu.au; fax: +61-2-98508313.
CiteULike 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati What's this?
This article has been cited by other articles:
|
|
 |
|
  N. Kumar and D. Mohanty MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes Nucleic Acids Res., July 13, 2007; 35(suppl_2): W549 - W555. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Tong, T. W. Tan, and S. Ranganathan Methods and protocols for prediction of immunogenic epitopes Brief Bioinform, March 1, 2007; 8(2): 96 - 108. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Tong, T. W. Tan, and S. Ranganathan In silico grouping of peptide/HLA class I complexes using structural interaction characteristics Bioinformatics, January 15, 2007; 23(2): 177 - 183. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. Zhang, C. Shao, D. Zheng, and Y. Gao An Integrated Machine Learning System to Computationally Screen Protein Databases for Protein Binding Peptide Ligands Mol. Cell. Proteomics, July 1, 2006; 5(7): 1224 - 1232. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. Donnes and O. Kohlbacher SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res., July 1, 2006; 34(Web Server issue): W194 - W197. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. C. Tong, G. L. Zhang, T. W. Tan, J. T. August, V. Brusic, and S. Ranganathan Prediction of HLA-DQ3.2{beta} Ligands: evidence of multiple registers in class II binding peptides Bioinformatics, May 15, 2006; 22(10): 1232 - 1238. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Madurga, I. Belda, X. Llora, and E. Giralt Design of enhanced agonists through the use of a new virtual screening method: Application to peptides that bind class I major histocompatibility complex (MHC) molecules Protein Sci., August 1, 2005; 14(8): 2069 - 2079. [Abstract] [Full Text] [PDF]
|
|
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
