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References:

  1. Tong JC, Kong L, Tan TW, Ranganathan S. 2006. MPID-T: database for sequence-structure-function information on T-cell receptor/peptide/MHC interactions. Appl Bioinformatics. 5, 111-114. PDF
  2. Govindarajan KR, Kangueane P, Tan TW, Ranganathan S. 2003. MPID: MHC-Peptide Interaction Database for sequence-structure-function information on peptides binding to MHC molecules. Bioinformatics. 19, 309-310.
  3. Khan JM, Tong JC, Ranganathan S. 2010. Structural Immunoinformatics: Understanding MHC-peptide-TR binding. In: Bioinformatics for Immunomics vol 3. (M.N. Davies, S. Ranganathan and D.R. Flower, Eds) Springer, New York, Chapter 7, 77-94.
  4. Kaas Q, Ruiz M, Lefranc MP. 2004. IMGT/3Dstructure-DB and IMGT/StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res. 32(Database issue), D208-210.
  5. Ehrenmann F, Kaas Q, Lefranc MP. 2010. IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. Nucleic Acids Res. 38(Database issue), D301-307.
  6. Robinson J, Waller MJ, Parham P, Bodmer JG, Marsh SG. 2001. IMGT/HLA Database-a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 29, 210-213.
  7. Khan JM, Ranganathan S. 2010. pDOCK: a new technique for rapid and accurate docking of peptide ligands to Major Histocompatibility Complexes. Immunome Res. 6(Suppl 1), S2.
  8. Tong JC, Tan TW, Ranganathan S. 2007. Methods and protocols for prediction of immunogenic epitopes. Brief Bioinform. 8(2), 96-108.
  9. Yewdell JW, Bennink JR. 1999. Immunodominance in major histocompatibility complex class I-restricted T lymphocyte responses. Annu Rev Immunol. 17, 51-88.
  10. Garcia KC, Adams JJ, Feng D, Ely LK. 2009. The molecular basis of TCR germline bias for MHC is surprisingly simple. Nat Immunol. 10, 143-147.
  11. Stewart-Jones G, Wadle A, Hombach A, Shenderov E, Held G, Fischer E, Kleber S, Stenner-Liewen F, Bauer S, McMichael A, Knuth A, Abken H, Hombach AA, Cerundolo V, Jones EY, Renner C. 2009. Rational development of high-affinity T-cell receptor-like antibodies. Proc Natl Acad Sci USA. 106, 5784-5788.
  12. Tong JC, Tan TW, Ranganathan S. 2007. In silico grouping of peptide/HLA class I complexes using structural interaction chracteristics. Bioinformatics. 23, 177-183.
  13. O'Brien C, Flower DR, Feighery C. 2008. Peptide length significantly influences in vitro affinity for MHC class II molecules. Immunome Res. 4, 6.
  14. Ritcher S, Wenzel A, Stein M, Gabdoulline RR, Wade RC. 2008. webPIPSA: a web server for the comparison of protein interaction properties. Nucleic Acids Res. 36, W276-280.
  15. Armstrong KM, Piepenbrink KH, Baker BM. 2008. Conformational changes and flexibility in T-cell receptor recognition of peptide-MHC complexes. Biochem J. 415, 183-196.
  16. Armstrong KM, Insaidoo FK, Baker BM. 2008. Thermodynamics of T-cell receptor-peptide/MHC interactions: progress and opportunities. J Mol Recognit. 21, 275-287.
  17. Varma R. 2008. TCR triggering by the pMHC complex: valency, affinity and dynamics. Sci Signal. 1, pe21.
  18. Mak TW. 2007. The T cell antigen receptor: "The Hunting of the Snark". Eur J Immunol. 37 Suppl 1, S83-93.
  19. Tong JC, Bramson J, Kanduc D, Chow S, Sinha AA, Ranganathan S. 2006. Modeling the bound conformation of Pemphigus vulgaris associated peptides to MHC Class II DR and DQ alleles. Immunome Res. 2, 1-10.
  20. Tong JC, Zhang GL, Tan TW, August JT, Brusic V, Ranganathan S. 2006. Prediction of HLA-DQ3.2beta ligands: evidence of multiple registers in class II binding peptides. Bioinformatics. 22, 1232-1238.
  21. Tong JC, Tan TW, Sinha AA, Ranganathan S. 2006. Prediction of desmoglein-3 peptides reveals multiple shared T-cell epitopes in HLA DR4- and DR6-associated pemphigus vulgaris. BMC Bioinformatics. 7 Suppl 5, S7.
  22. Rudolph MG, Stanfield RL, Wilson IA. 2006. How TCRs bind MHCs, peptides and coreceptors. Annu Rev Immunol. 24, 419-466.
  23. Gille C, Robinson PN. 2006. HotSwap for bioinformatics: A STRAP tutorial. BMC Bioinformatics. 7, 64-70.
  24. Tong JC, Tan TW, Ranganathan S. 2004. Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci. 13, 2523-2532.
  25. Fernandez-Recio J, Totrov M, Abagyan R. 2003. ICM-DISCO docking by Global Energy Optimization with Fully Flexible Side-Chains. Proteins. 52, 113-117.
  26. Abagyan RA, Maxim T. 1999. Ab Initio folding of peptides by the Optimal-Bias Monte Carlo Minimization Procedure. J Comput Phys. 151, 402-421.
  27. Abagyan RA, Totrov MM. 1997. Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J Mol Biol. 268, 678-685.
  28. McCoy AJ, Chandana Epa V, Colman PM. 1997. Electrostatic complementarity at protein/protein interfaces. J Mol Biol. 268, 570-584.
  29. Sali A, Blundell TL. 1993. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 234, 779-815.
  30. Wilson IA. 1999. Perspectives: protein structure. Class conscious TCR? Science. 286, 1867-1868.
  31. Robinson J, Waller MJ, Parham P, Bodmer JG, Marsh SGE. 2001. IMGT/HLA Database - a sequence database for the human major histocompatibility complex. Nucleic Acids Res. 29, 210-213.
  32. Zhang C, Anderson A, DeLisi C. 1998. Structural principles that govern the peptide binding motifs of class I MHC molecules. J. Mol. Biol. 281, 929-947.
  33. Rammensee H, Bachmann J, Emmerich NP, Bachor A, Stevanovic S. 1999. SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics. 50, 213-219.
  34. Brusic V, Rudy G, Harrison LC. 1998. MHCPEP, a database of MHC-binding peptides: update 1997. Nucleic Acids Res. 26, 368-71.
  35. Andersen MH, Tan L, Sondergaard I, Zeuthen J, Elliott T, Haurum JS. 2000. Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules. Tissue Antigens. 55, 519-31.
  36. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. 2000. The Protein data bank. Nucleic Acids Res. 28, 235-242.
  37. Kangueane P, Sakharkar MK, Kolatkar PR, Ren EC. 2001. Towards the MHC-Peptide combinatorics. Hum Immunol. 62, 539-56.
  38. Kangueane P, Sakharkar MK, Lim KS, Hao H, Lin K, Ren EC, Kolatkar PR. 2000. Knowledge-based grouping of modeled HLA-peptide complexes. Hum Immunol. 61,460-66.
  39. Subieta K, Plodzien J. 2001. Object Views and Query Modification. In Barzdins J, Caplinskas A (eds.), Databases and Information Systems. Kluwer Academic Publishers, Dordrecht, pp. 3-14.
  40. Jones S, Thornton JM. 1996. Principles of protein-protein interactions. Proc Natl Acad Sci USA. 93, 13-20.
  41. Abagyan RA, Totrov MM, Kuznetsov DA. 1994. ICM: a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J Comp Chem. 15, 488-506.
  42. Abagyan RA, Totrov MM, 1994. Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations For Peptides and Proteins. J Mol Biol. 235, 983-1002.
  43. McDonald IK, Thornton JM. 1994. Satisfying hydrogen bonding potential in proteins. J Mol Biol. 238, 777-793.
  44. Laskowski RA. 1995. SURFNET: a program for visualizing molecular surfaces, cavities and intermolecular interactions. J Mol Graph. 13, 323-330.
  45. Hubbard SJ, Thornton JM. 1993. 'NACCESS', Computer Program, Department of Biochemistry and Molecular Biology, University College London, UK
  46. Wallace AC, Laskowski RA, Thornton JM. 1995. LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134.
  47. Crooks GE, Hon G, Chandonia JM, Brenner SE. 2004. WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190.
  48. Liu S, Zhang C, Zhou H, Zhou Y. 2004. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins. 56, 93-101.
  49. MacSparron H, Blythe MJ, Zygouri C, Doytchinova IA, Flower DR. 2003. JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci. 43,1276-1287.
  50. Blythe MJ, Doytchinova IA, Flower DR. 2002. JenPep: a database of quatitative functional peptide data for immunology. Bioinformatics. 18,434.439.