Sette A, Newman M, Livingston B, McKinney D, Sidney J, Ishioka G, Tangri S, Alexander J, Fikes J, Chestnut R: Optimizing vaccine design for cellular processing, MHC binding and TCR recognition. Tissue Antigens 2002, 59: 443–451. 10.1034/j.1399-0039.2002.590601.x
Article
CAS
PubMed
Google Scholar
Craiu A, Akopian T, Goldberg A, Rock KL: Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide. Proc Natl Acad Sci USA 1997, 94: 10850–10855. 10.1073/pnas.94.20.10850
Article
PubMed Central
CAS
PubMed
Google Scholar
Mo XY, Cascio P, Lemerise K, Goldberg AL, Rock K: Distinct proteolytic processes generate the C and N termini of MHC class I-binding peptides. J Immunol 1999, 163: 5851–5859.
CAS
PubMed
Google Scholar
Serwold T, Shastri N: Specific proteolytic cleavages limit the diversity of the pool of peptides available to MHC class I molecules in living cells. J Immunol 1999, 162: 4712–4719.
CAS
PubMed
Google Scholar
Cascio P, Hilton C, Kisselev AF, Rock KL, Goldberg AL: 26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide. EMBO J 2001, 20: 2357–2366. 10.1093/emboj/20.10.2357
Article
PubMed Central
CAS
PubMed
Google Scholar
Orlowski M, Michaud C: Pituitary multicatalytic proteinase complex. Specificity of components and aspects of proteolitic activity. Biochemistry 1989, 28: 9270–9278. 10.1021/bi00450a006
Article
CAS
PubMed
Google Scholar
Djaballah H, Harness JA, Savory PJ, Rivett AJ: Use of serine-protease inhibitors as probes for the different proteolytic activities of the rat liver multicatalitic proteinase complex. Eur J Biochem 1992, 209: 629–634. 10.1111/j.1432-1033.1992.tb17329.x
Article
CAS
PubMed
Google Scholar
Orlowski M, Cardozo C, Michaud C: Evidence for the presence of five distinct proteolytic components in the pituitary multicatalytic proteinase complex. Properties of two components cleaving bonds on the carboxy side of branched chain and small neutral amino acids. Biochemistry 1993, 32: 1563–1572. 10.1021/bi00057a022
Article
CAS
PubMed
Google Scholar
Tanaka K, Kasahara M: The MHC class I ligand-generating system: roles of immunoproteasomes and the interferon-γ-inducible proteasome activator PA28. Immunol Rev 1998, 163: 161–176.
Article
CAS
PubMed
Google Scholar
Van den Eynde BJ, Morel S: Differential processing of class-I-restricted epitopes by the standard proteasome and the immunoproteasome. Curr Opin Immunol 2001, 13: 147–153. 10.1016/S0952-7915(00)00197-7
Article
CAS
PubMed
Google Scholar
Toes RE, Nussbaum AK, Degermann S, Schirle M, Emmerich NP, Kraft M, Laplace C, Zwinderman A, Dick TP, Muller J, Schonfisch B, Schmid C, Fehling HJ, Stevanovic S, Rammensee H-G, Schild H: Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. J Exp Med 2001, 194: 1–12. 10.1084/jem.194.1.1
Article
PubMed Central
CAS
PubMed
Google Scholar
Rammensee H-G, Friede T, Stevanović S: MHC ligands and peptide motifs: first listing. Immunogenetics 1995, 41: 178–228. 10.1007/BF00172063
Article
CAS
PubMed
Google Scholar
Monaco J, Cho S, Attaya M: Transport protein genes in the murine MHC – possible implications for antigen processing. Science 1990, 250: 1723–1726.
Article
CAS
PubMed
Google Scholar
Meyer TH, van Endert PM, Uebel S, Ehring B, Tampé R: Functional expression and purification of the ABC transporter complex associated with antigen processing (TAP) in insect cells. FEBS Lett 1994, 351: 443–447. 10.1016/0014-5793(94)00908-2
Article
CAS
PubMed
Google Scholar
Müller KM, Ebensperger C, Tampé R: Nucleotide binding to the hydrophilic C-terminal domain of the transporter associated with antigen processing (TAP). J Biol Chem 1994, 269: 14032–14037.
PubMed
Google Scholar
Schumacher TNM, Kantesaria DV, Heemels MT, Ashton-Rickardt PG, Shepherd JC, Früh K, Yang Y, Peterson PA, Tonegawa S, Ploegh HL: Peptide length and sequence specificity of the mouse TAP1/TAP2 translocator. J Exp Med 1994, 179: 533–540. 10.1084/jem.179.2.533
Article
CAS
PubMed
Google Scholar
Lautscham G, Rickinson A, Blake N: TAP-independent antigen presentation on MHC class I molecules: lessons from Epstein-Barr virus. Microbes Infect 2003, 5: 291–299. 10.1016/S1286-4579(03)00031-5
Article
CAS
PubMed
Google Scholar
Brusic V, van Endert P, Zeleznikow J, Daniel S, Hammer J, Petrovsky N: A neural network model approach to the study of human TAP transporter. In Silico Biology 1998, 1: 10. [http://www.bioinfo.de/isb/1998/01/0010/]
Google Scholar
de la Salle H, Houssaint E, Peyrat MA, Arnold D, Salamero J, Pinczon D, Stevanovic S, Bausinger H, Fricker D, Gomard E, Biddison W, Lehner P, UytdeHaag F, Sasporte M, Donato L, Rammensee HG, Cazenave JP, Hanau D, Tongio MM, Bonneville M: Human peptide transporter deficiency: importance of HLA-B in the presentation of TAP-independent EBV antigens. J Immunol 1997, 158: 4555–4563.
CAS
PubMed
Google Scholar
Mormung F, Neefjes JJ, Hämmerling GJ: Peptide selection by MHC-encoded TAP transporters. Curr Opin Immunol 1994, 6: 32–37. 10.1016/0952-7915(94)90030-2
Article
Google Scholar
Henderson RA, Michel H, Sakaguchi K, Shabanowitz J, Appella E, Hunt DF, Engelhard VH: HLA-A2.1-associated peptides from a mutant cell line: a second pathway of antigen presentation. Science 1992, 255: 1264–1266.
Article
CAS
PubMed
Google Scholar
Guéguen M, Biddison W, Long EO: T cell recognition of an HLA-A2-restricted epitope derived from a cleaved signal sequence. J Exp Med 1994, 180: 1989–1994. 10.1084/jem.180.5.1989
Article
PubMed
Google Scholar
Smith KD, Lutz CT: Peptide-dependent expression of HLA-B7 on antigen processing-deficient T2 cells. J Immunol 1996, 156: 3755–3764.
CAS
PubMed
Google Scholar
Khanna R, Burrows SR, Moss DJ, Silins SL: Peptide transporter (TAP-1 and TAP-2)-independent endogenous processing of Epstein-Barr virus (EBV) latent membrane protein 2A: implications for cytotoxic T-lymphocyte control of EBV-associated malignancies. J Virol 1996, 70: 5357–5362.
PubMed Central
CAS
PubMed
Google Scholar
Janeway CA Jr, Travers P, Walport M, Capra JD: Immunobiology. The immune system in health and desease. London, Current Biology Publications; 1999.
Google Scholar
Saper MA, Bjorkman PJ, Wiley DC: Refined structure of the human histocompatibility antigen HLA-A2 at 2.6 A resolution. J Mol Biol 1991, 219: 277–319. 10.1016/0022-2836(91)90567-P
Article
CAS
PubMed
Google Scholar
Smith KJ, Reid SW, Harlos K, McMichael AJ, Stuard DI, Bell JI, Jones EY: Bound water structure and polymorphic amino acids act together to allow the binding of different peptides to MHC class I HLA-B53. Immunity 1996, 4: 215–228. 10.1016/S1074-7613(00)80430-6
Article
CAS
PubMed
Google Scholar
Fan QR, Wiley DC: Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor. J Exp Med 1999, 190: 113–123. 10.1084/jem.190.1.113
Article
PubMed Central
CAS
PubMed
Google Scholar
Flower DR: Towards in silico prediction of immunogenic epitopes. Trends Immunol 2003, 24: 667–674. 10.1016/j.it.2003.10.006
Article
CAS
PubMed
Google Scholar
Golgberg AL, Cascio P, Saric T, Rock KL: The importance of the proteasome and subsequent proteolitic steps in the generation of antigenic peptides. Mol Immunol 2002, 39: 147–164. 10.1016/S0161-5890(02)00098-6
Article
Google Scholar
Schirle M, Weinschenk T, Stevanović S: Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens. J Immunol Methods 2001, 257: 1–16. 10.1016/S0022-1759(01)00459-8
Article
CAS
PubMed
Google Scholar
DeLisi C, Berzofski JA: T-cell antigenic sites tend to be amphipathic structures. Proc Natl Acad Sci USA 1985, 82: 7048–7052.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rothbard JB, Taylor WR: A sequence pattern common to T cell epitopes. EMBO J 1988, 7: 93–100.
PubMed Central
CAS
PubMed
Google Scholar
Meister GE, Roberts CG, Berzofsky JA, De Groot AS: Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences. Vaccine 1995, 13: 581–591. 10.1016/0264-410X(94)00014-E
Article
CAS
PubMed
Google Scholar
Deavin AJ, Auton TR, Greaney PJ: Statistical comparison of established T cell epitope predictors against a large database of human and murine antigens. Mol Immunol 1996, 33: 145–155. 10.1016/0161-5890(95)00120-4
Article
CAS
PubMed
Google Scholar
Flower DR, Doytchinova IA, Paine K, Taylor P, Blythe MJ, Lamponi D, Zygouri C, Guan P, McSparron H, Kirkbride H: Computational Vaccine Design. In Drug Design. Cutting Edge Approaches. Edited by: Flower DR. RSC; 2002:136–180.
Google Scholar
Sette A, Buus E, Appella JA, Smith R, Chesnut R, Miles C, Colon SM, Grey HM: Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc Nat Acad sci USA 1989, 86: 3296–3300.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rammensee H, Bachmann J, Emmerich NP, Bachor OA, Stevanovic S: SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 1999, 50: 213–219. [http://www.syfpeithi.de] 10.1007/s002510050595
Article
CAS
PubMed
Google Scholar
Reche PA, Glutting JP, Reinherz EL: Prediction of MHC class I binding peptides using profile motifs. Hum Immunol 2002, 63: 701–709. 10.1016/S0198-8859(02)00432-9
Article
CAS
PubMed
Google Scholar
Reche PA, Glutting JP, Reinherz EL: Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004, 56: 405–419. 10.1007/s00251-004-0709-7
Article
CAS
PubMed
Google Scholar
Marshall KW, Wilson KJ, Liang J, Woods A, Zaller D, Rothbard JB: Prediction of peptide affinity to HLA-DRB1*0401. J Immunol 1995, 154: 5927–5933.
CAS
PubMed
Google Scholar
Doytchinova IA, Blythe MJ, Flower DR: Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201. J Proteome Res 2002, 1: 263–272. 10.1021/pr015513z
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Flower DR: Towards the in silico identification of class II restricted T cell epitopes: a partial least squares iterative self-consistent algorithm for affinity prediction. Bioinformatics 2003, 19: 2263–2270. 10.1093/bioinformatics/btg312
Article
CAS
PubMed
Google Scholar
Bisset LR, Fierz W: Using a neutral network to identify potential HLA-DR1 binding sites within proteins. J Mol Recognit 1993, 6: 41–48. 10.1002/jmr.300060105
Article
CAS
PubMed
Google Scholar
Gulukota K, DeLisi C: Neural network method for predicting peptides that bind major histocompatibility complex molecules. Methods Mol Biol 2001, 156: 201–209.
CAS
PubMed
Google Scholar
Honeyman MC, Brusic V, Stone NL, Harrison LC: Neural network-based prediction of candidate T-cell epitopes. Nat Biotechnol 1998, 16: 966–969. 10.1038/nbt1098-966
Article
CAS
PubMed
Google Scholar
Brusic V, Rudy G, Honeyman G, Hammer J, Harrison L: Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics 1998, 14: 121–130. 10.1093/bioinformatics/14.2.121
Article
CAS
PubMed
Google Scholar
Rognan D, Lauemoller SL, Holm A, Buus S, Tschinke V: Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J Med Chem 1999, 42: 4650–4658. 10.1021/jm9910775
Article
CAS
PubMed
Google Scholar
Altuvia Y, Schueler O, Margalit H: Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 1995, 249: 244–250. 10.1006/jmbi.1995.0293
Article
CAS
PubMed
Google Scholar
Doytchinova I, Flower DR: Towards the quantitative prediction of T-cell epitopes: CoMFA and CoMSIA studies of peptides with affinity to class I MHC molecule HLA-A*0201. J Med Chem 2001, 44: 3572–3581. 10.1021/jm010021j
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Flower DR: A Comparative Molecular Similarity Index Analysis (CoMSIA) study identifies an HLA-A2 binding supermotif. J Comput-Aid Mol Des 2002, 16: 535–544. 10.1023/A:1021917203966
Article
CAS
Google Scholar
Guan P, Doytchinova IA, Flower DR: HLA-A3-supermotif defined by quantitative structure-activity relationship analysis. Protein Eng 2003, 16: 11–18. 10.1093/proeng/gzg005
Article
CAS
PubMed
Google Scholar
Dönnes P, Elofsson A: Prediction of MHC class I binding peptides using SVMHC. BMC Bioinformatics 2002, 3: 25. 10.1186/1471-2105-3-25
Article
PubMed Central
PubMed
Google Scholar
Zhao Y, Pinilla C, Valmori D, Martin R, Simon R: Application of support vector machines for T-cell epitope predictions. Bioinformatics 2003, 19: 1978–1984. 10.1093/bioinformatics/btg255
Article
CAS
PubMed
Google Scholar
Holzhutter HG, Frommel C, Kloetzel PM: A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20S proteasome. J Mol Biol 1999, 286: 1251–1265. 10.1006/jmbi.1998.2530
Article
CAS
PubMed
Google Scholar
Kuttler C, Nussbaum AK, Dick TP, Rammensee H-G, Schild H, Hadeler K-P: An algorithm for the prediction of proteasome cleavages. J Mol Biol 2000, 298: 417–429. 10.1006/jmbi.2000.3683
Article
CAS
PubMed
Google Scholar
Keşmir C, Nussbaum AK, Schild H, Detours V, Brunak S: Prediction of proteasome cleavage motifs by neural networks. Protein Eng 2002, 15: 287–296. 10.1093/protein/15.4.287
Article
PubMed
Google Scholar
Uebel S, Meyer TH, Kraas W, Kienle S, Jung G, Wiesmüller KH, Tampé R: Requirements for peptide binding to the human transporter associated with antigen processing revealed by peptide scans and complex peptide libraries. J Biol Chem 1995, 270: 18512–18516. 10.1074/jbc.270.31.18512
Article
CAS
PubMed
Google Scholar
Daniel S, Brusic V, Caillat-Zucman S, Petrovsky N, Harrison L, Riganelli D, Sinigaglia F, Gallazzi F, Hammer J, van Endert PM: Relationship between peptide selectivities of human transporters associated with antigen processing and HLA class I molecules. J Immunol 1998, 161: 617–624.
CAS
PubMed
Google Scholar
Peters B, Bulik S, Tampé R, van Endert PM, Holzhütter HG: Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol 2003, 171: 1741–1749.
Article
CAS
PubMed
Google Scholar
Bhasin M, Raghava GPS: Analysis and prediction of affinity of TAP binding peptides using cascade SVM. Protein Sci 2004, 13: 596–607. 10.1110/ps.03373104
Article
PubMed Central
CAS
PubMed
Google Scholar
Hakenberg J, Nussbaum AK, Schild H, Rammensee HG, Kuttler C, Holzhutter HG, Kloetzel PM, Kaufmann SHE, Mollenkopf HJ: MAPPP: MHC class I antigenic peptide processing prediction. Appl Bioinformatics 2003, 2: 155–158.
CAS
PubMed
Google Scholar
Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhütter HG: Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci 2005, 62: 1025–1037. 10.1007/s00018-005-4528-2
Article
CAS
PubMed
Google Scholar
Peters B, Sette A: Generating quantitative models describing the sequence specificity of biological process with the stabilized matrix method. BMC Bioinformatics 2005, 6: 132. [http://www.mhc-pathway.net] 10.1186/1471-2105-6-132
Article
PubMed Central
PubMed
Google Scholar
Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M: An integrative approach to CTL epitope prediction: A combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol 2005, 35: 2295–2303. [http://www.cbs.dtu.dk/services/NetCTL] 10.1002/eji.200425811
Article
CAS
PubMed
Google Scholar
Dönnes P, Kohlbacher O: Integrated modeling of the major events in the MHC class I antigen processing pathway. Protein Sci 2005, 14: 2132–2140. [http://www-bs.informatik.uni-tuebingen.de/WAPP] 10.1110/ps.051352405
Article
PubMed Central
PubMed
Google Scholar
Guan P, Doytchinova I, Hattotuwagama C, Flower DR: MHCPred 2.0, an updated quantitative T cell epitope prediction server. Appl Bioinformatics 2006, 5: 55–61.
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Walshe VA, Jones NA, Gloster SE, Borrow P, Flower DR: Coupling in silico and in vitro analysis of peptide-MHC binding: A Bioinformatic approach enabling prediction of superbinding peptides and anchorless epitopes. J Immunol 2004, 172: 7495–7502.
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Hemsley S, Flower DR: Transporter associated with antigen processing preselection of peptides binding to the MHC: A Bioinformatic evaluation. J Immunol 2004, 173: 6813–6819.
Article
CAS
PubMed
Google Scholar
Doytchinova IA, Flower DR: Class I T cell epitope prediction: improvements using a combination of Proteasome cleavage, TAP affinity, and MHC binding. Mol Immun 2006, in press.
Google Scholar
EpiJen server for T cell epitope prediction[http://www.jenner.ac.uk/EpiJen]
Doytchinova IA, Flower DR: The HLA-A2-supermotif: A QSAR definition. Org & Biomol Chem 2003, 1: 2648–2654. 10.1039/b300707c
Article
CAS
Google Scholar
Toseland CP, Taylor DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova IA, Guan P, Hattotuwagama CK, Flower DR: AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 2005, 1: 4. http://www.immunome-research.com/content/1/1/4, http://www.jenner.ac.uk/AntiJen 10.1186/1745-7580-1-4
Article
PubMed Central
PubMed
Google Scholar
Free SM Jr, Wilson JW: A mathematical contribution to structure – activity studies. J Med Chem 1964, 53: 395–399. 10.1021/jm00334a001
Article
Google Scholar
Wold S: PLS for Multivariate Linear Modeling. In Chemometric Methods in Molecular Design Edited by: Van der Waterbeemd H, Weinheim VCH. 1995, 195–218.
Google Scholar
Vinitsky A, Anton LC, Snyder HL, Orlowski M, Bennink JR, Yewdell JW: The generation of MHC class I-associated peptides is only partially inhibited by proteasome inhibitors: involvement of nonproteasomal cytosolic proteases in antigen processing. J Immunol 1997, 159: 554–564.
CAS
PubMed
Google Scholar
Luckey CJ, King GM, Marto JA, Venketeswaran S, Maier BF, Crotzer VL, Colella TA, Shabanowitz J, Hunt DF, Engelhard VH: Proteasomes can either generate or destroy MHC class I epitopes: evidence for nonproteosomal epitope generation in the cytosol. J Immunol 1998, 161: 112–121.
CAS
PubMed
Google Scholar
Luckey CJ, Marto JA, Partridge M, Hall E, White FM, Lippolis JD, Shabanowitz J, Hunt DF, Engelhard VH: Differences in the expression of human class I MHC alleles and their associated peptides in the presence of proteasome inhibitors. J Immunol 2001, 167: 1212–1221.
Article
CAS
PubMed
Google Scholar
Geier E, Pfeifer G, Wilm M, Lucchiari-Hartz M, Baumeister W, Eichmann K, Niedermann G: A giant protease with potential to substitute for some functions of the proteasome. Science 1999, 283: 978–981. 10.1126/science.283.5404.978
Article
CAS
PubMed
Google Scholar
Beninga J, Rock KL, Goldberg AL: Interferon-gamma can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase. J Biol Chem 1998, 273: 18734–18742. 10.1074/jbc.273.30.18734
Article
CAS
PubMed
Google Scholar
Stoltze L, Schirle M, Schwarz G, Schroeter C, Thompson MW, Hersh LB, Kalbacher H, Stevanović S, Rammensee H-G, Schild H: Two new proteases in the MHC class I processing pathway. Nat Immunol 2000, 1: 413–418. 10.1038/80852
Article
CAS
PubMed
Google Scholar
Serwold T, Gonzalez F, Kim J, Jacob R, Shastri N: ERAAP customizes peptides for MHC class I molecules in the endoplasmic reticulum. Nature 2002, 419: 480–483. 10.1038/nature01074
Article
CAS
PubMed
Google Scholar
Saric T, Chang S-C, Hattori A, York IA, Markant S, Rock KL, Tsujimoto M, Goldberg AL: An IFN-γ-induced aminopeptidase in the ER, ERAPI, trims precursors to MHC class I-presented peptides. Nat Immunol 2002, 3: 1169–1176. 10.1038/ni859
Article
CAS
PubMed
Google Scholar
York IA, Chang S-C, Saric T, Keys JA, Favreau JM, Goldberg AL, Rock KL: The ER aminopeptidase ERAPI enhances or limits antigen presentation by trimming epitopes to 8–9 residues. Nat Immunol 2002, 3: 1177–1184. 10.1038/ni860
Article
CAS
PubMed
Google Scholar
Hanada K, Yewdell JW, Yang JC: Immune recognition of a human renal cancer antigen through post-translational protein splicing. Nature 2004, 427: 252–256. 10.1038/nature02240
Article
CAS
PubMed
Google Scholar
Vigneron N, Stroobant V, Chapiro J, ooms A, Degiovanni G, Morel S, van der Bruggen P, Boon T, van den Eynde BJ: An antigenic peptide produced by peptide splicing in the proteasome. Science 2004, 304: 587–590. 10.1126/science.1095522
Article
CAS
PubMed
Google Scholar
Hattotuwagama CK, Guan P, Doytchinova IA, Zygouri C, Flower DR: Quantitative online prediction of peptide binding to the major histocompatibility complex. J Mol Graph Model 2004, 22: 195–207. 10.1016/S1093-3263(03)00160-8
Article
CAS
PubMed
Google Scholar
SYBYL 6.9 Tripos Inc., St. Louis; 2004.
Bradley AP: The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recognition 1997, 30: 1145–1159. 10.1016/S0031-3203(96)00142-2
Article
Google Scholar
Barnard JM, Downs GM: Clustering of chemical structures on the basis of two-dimensional similarity measures. J Chem Inf Comput Sci 1992, 32: 644–649. 10.1021/ci00010a010
Article
CAS
Google Scholar
Brown RD, Martin YC: Use of structure-activity data to compare structure-based clustering methods and descriptors for use in compound selection. J Chem Inf Comput Sci 1996, 36: 572–584. 10.1021/ci9501047
Article
CAS
Google Scholar
HIV Molecular Immunology Database[http://www.hiv.lanl.gov]
Schirmbeck R, Riedl P, Fissolo N, Lemonnier FA, Bertoletti A, Reimann J: Translation from cryptic reading frames of DNA vaccines generates an extended repertoire of immunogenic, MHC class I-restricted epitopes. J Immunol 2005, 174: 4647–4656.
Article
CAS
PubMed
Google Scholar
Schwab SR, Shugart JA, Horng T, Malarkannan S, Shastri N: Unanticipated Antigens: Translation Initiation at CUG with Leucine. PLoS Biol 2004, 2(11):e366. 10.1371/journal.pbio.0020366
Article
PubMed Central
PubMed
Google Scholar