Name
Title | ||
|---|---|---|
Prediction of HLA-DQ3.2β Ligands: evidence of multiple registers in class II binding peptides |
Abstract | ||
|---|---|---|
Motivation: While processing of MHC class II antigens for presentation to helper T-cells is essential for normal immune response, it is also implicated in the pathogenesis of autoimmune disorders and hypersensitivity reactions. Sequence-based computational techniques for predicting HLA-DQ binding peptides have encountered limited success, with few prediction techniques developed using three-dimensional models. Methods: We describe a structure-based prediction model for modeling peptide-DQ3.2β complexes. We have developed a rapid and accurate protocol for docking candidate peptides into the DQ3.2β receptor and a scoring function to discriminate binders from the background. The scoring function was rigorously trained, tested and validated using experimentally verified DQ3.2β binding and non-binding peptides obtained from biochemical and functional studies. Results: Our model predicts DQ3.2β binding peptides with high accuracy [area under the receiver operating characteristic (ROC) curve AROC 0.90], compared with experimental data. We investigated the binding patterns of DQ3.2β peptides and illustrate that several registers exist within a candidate binding peptide. Further analysis reveals that peptides with multiple registers occur predominantly for high-affinity binders. Contact: shoba@els.mq.edu.au Supplementary information: Supplementary data is available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2006 | 10.1093/bioinformatics/btl071 | Bioinformatics (Oxford, England) |
Keywords | Field | DocType |
hla-dq binding peptides,structure-based prediction model,non-binding peptides,binding peptides,prediction technique,candidate binding peptide,binding pattern,docking candidate peptides,class ii,scoring function,multiple register,experimental data,three dimensional,prediction model,score function,receiver operator characteristic,immune response,mathematics | Receiver operating characteristic,Antigen,Computer science,Docking (dog),Peptide,Major histocompatibility complex,Bioinformatics,Human leukocyte antigen,HLA-DR,MHC class II | Journal |
Volume | Issue | ISSN |
22 | 10 | 1367-4803 |
Citations | PageRank | References |
10 | 0.91 | 6 |
Authors | ||
6 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Joo Chuan Tong | 1 | 182 | 9.00 |
| G.L. Zhang | 2 | 208 | 16.91 |
| Tin Wee Tan | 3 | 566 | 36.14 |
| J. Thomas August | 4 | 143 | 7.36 |
| Vladimir Brusic | 5 | 551 | 63.37 |
| Shoba Ranganathan | 6 | 689 | 36.60 |