Toward the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity for the class I MHC molecule HLA-A*0201

Journal of Medicinal Chemistry

Volumn 44, Issue 22, 2001, Pages 3572-3581

  Doytchinova, I A ^a,b   Flower, D R ^a  

^a UK   (United Kingdom)

^b MEDICAL UNIVERSITY OF SOFIA   (Bulgaria)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE; HLA A ANTIGEN; MAJOR HISTOCOMPATIBILITY ANTIGEN CLASS 1; PEPTIDE;

ANTIGEN BINDING; ARTICLE; BINDING AFFINITY; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR MODEL; PHYSICAL CHEMISTRY; PREDICTION; PROTEIN BINDING; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUANTITATIVE ASSAY; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STEREOCHEMISTRY; T LYMPHOCYTE; TECHNIQUE;

AMINO ACID SEQUENCE; EPITOPES; HLA-A ANTIGENS; HYDROGEN BONDING; MODELS, MOLECULAR; PEPTIDES; PROTEIN BINDING; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; T-LYMPHOCYTES;

EID: 0035950043     PISSN: 00222623     EISSN: None     Source Type: Journal    
DOI: 10.1021/jm010021j     Document Type: Article

References (63)

1. Identification of self-peptides bound to purified HLA-B27
2. Sequence analysis of peptides bound to MHC class II molecules
3. Molecular interactions between extracellular components of the T-cell receptor signaling complex
4. Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium
5. HLA class I region sequences
6. Allele and haplotype frequencies for HLA and complement loci in various ethnic groups
7. Interethnic genetic differentiation in Africa: HLA class I antigens in the Gambia
8. World distribution of HLA alleles and implications for disease
9. Breast and ovarian cancer-specific cytotoxic T lymphocytes recognize the same HER2/neu-derived peptide
10. Influenza virus-specific cytotoxic T lymphocytes recognize HLA-molecules. Blocking by monoclonal anti-HLA antibodies
11. Tumor-specific lysis of human renal cell carcinomas by tumor-infiltrating lymphocytes. I. HLA-A2-restricted recognition of autologous and allogeneic tumor lines
12. Identification of new HER2/neu-derived peptide epitopes that can elicit specific CTL against autologous and allogeneic carcinomas and melanomas
13. Induction of tumor-reactive CTL from peripheral blood and tumor-infiltrating lymphocytes of melanoma patients by in vitro stimulation with an immunodominant peptide of the human melanoma antigen MART1
14. Identification of a shared HLA-A*0201-restricted T-Cell epitope from the melanoma antigen tyrosinase-related protein 2 (TRP2)
15. Refined structure of the human histocompatibility antigen HLA-A2 at 26 Å resolution
16. The antigenic identity of peptide-MHC Complexes: A comparison of the conformations of five viral peptides presented by HLA-A2
17. Peptide binding to the most frequent HLA-A class I alleles measured by quantitative molecular binding assays
18. Prominent role of secondary anchor residues in peptide binding to HLA-A*0201 molecules
19. Definition of specific peptide motifs for four major HLA-A alleles
20. Sequence motifs important for peptide binding to the human MHC class I molecule, HLA-A2
21. Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains
22. Allele specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
23. The three-dimensional structure of peptide-MHC complexes
24. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
25. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
26. Comparative molecular similarity index analysis (CoMSIA) to study hydrogen-bonding properties and to score combinatorial libraries
27. Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa
28. Pole of HLA-A motifs in identification of potential CTL epitopes in human papillomavirus Type 16 E6 and E7 proteins
29. The relationship between class I binding affinity and immunogenicity of potential cytotoxic T cell epitopes
30. Improved induction of melanoma-reactive CTL with peptides from the melanoma antigen gp100 modified at HLA-A*0201-binding residues
31. Comparison of cytotoxic T lymphocyte responses induced by peptide or DNA immunization: Implications on immunogenicity and immunodominance
32. Binding of a peptide antigen to multiple HLA alleles allows definition of an A2-like supertype
33. Identification of subdominant CTL epitopes of the GP100 melanoma-associated tumor antigen by primary in vitro immunization with peptide-pulsed dendritic cells
34. Recognition of multiple epitopes in the human melanoma antigen gp100 by tumor-infiltrating T lymphocytes associated with in vivo tumor regression
35. Restart procedures for the conjugate gradient method
36. AM1: A new general purpose quantum mechanical molecular model
37. Crossvalidation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies
38. Positioning of a peptide in the cleft of HLA-A2 by complementing amino acid changes
39. CoMFA: Scope and limitations
40. The structural basis for the increased immunogenicity of two HIV-reverse transcriptase peptide variant/class I major histocompatibility complexes
41. A general strategy to enhance immunogenicity of low-affinity HLA-A2.1-associated peptides: Implication in the identification of criptic tumor epitopes
42. Enhanced in vitro potency and in vivo immunogenicity of a CTL epitope from hepatitis C virus core protein following amino acid replacement at secondary HLA-A2.1 binding positions
43. MHC ligands and peptide motifs: First listing
44. SYFPEITHI: Database for MHC ligands and peptide motifs
45. An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries
46. Use of global amino acid replacements to define the requirements for MHC binding and T cell recognition of moth cytochrome C (93-103)
47. A road map for HLA-A, HLA-B, and HLA-C peptide binding specificities
48. Knowledge-based grouping of modeled HLA peptide complexes
49. A geometric study of the amino acid sequence of class I HLA molecules
50. Molecular dynamics simulation of MHC-peptide complexes as a tool for predicting potential T cell epitopes
51. Free energy mapping of class I MHC molecules and structural determination of bound peptides
52. Magnitude of structural changes of the T-cell receptor binding regions determine the strength of T-cell antagonism: Molecular dynamics simulations of HLA-DR4 (DRBi*0405) complexed with analogue peptide
53. On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
54. Two complementary methods for predicting peptides binding major histocompatibility complex molecules
55. Prediction of MHC Class II-binding peptides using an evolutionary algorithm and artificial neural network
56. Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models
57. Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm
58. Predicting binding affinities of protein ligands from three-dimensional models: Application to peptide binding to class I major histocompatibility proteins
59. Structure-based prediction of binding peptides to MHC class I molecules: Application to a broad range of MHC alleles
60. The importance of secondary anchor residue motifs of HLA class I proteins: A chemometric approach
61. New chemical descriptors relevant for the design of biologically active peptides. A multivariate characterization of 87 amino acids