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Volumn 7, Issue 8, 2012, Pages

Predicting HLA class I non-permissive amino acid residues substitutions

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; HLA ANTIGEN CLASS 1;

EID: 84864646210     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0041710     Document Type: Article
Times cited : (22)

References (55)
  • 1
    • 0033301381 scopus 로고    scopus 로고
    • Polymorphism and evolution of HLA class I and II genes and molecules
    • Little AM, Parham P, (1999) Polymorphism and evolution of HLA class I and II genes and molecules. Rev Immunogenet 1: 105-123.
    • (1999) Rev Immunogenet , vol.1 , pp. 105-123
    • Little, A.M.1    Parham, P.2
  • 2
    • 34247573902 scopus 로고    scopus 로고
    • Graft-versus-host disease
    • Shlomchik WD, (2007) Graft-versus-host disease. Nat Rev Immunol 7: 340-352.
    • (2007) Nat Rev Immunol , vol.7 , pp. 340-352
    • Shlomchik, W.D.1
  • 4
    • 0041989751 scopus 로고    scopus 로고
    • CASTp: Computed Atlas of Surface Topography of proteins
    • Binkowski TA, Naghibzadeh S, Liang J, (2003) CASTp: Computed Atlas of Surface Topography of proteins. Nucleic Acids Res 31: 3352-3355.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3352-3355
    • Binkowski, T.A.1    Naghibzadeh, S.2    Liang, J.3
  • 5
    • 0030926140 scopus 로고    scopus 로고
    • Crystal structure of the complex between human CD8alpha(alpha) and HLA-A2
    • Gao GF, Tormo J, Gerth UC, Wyer JR, McMichael AJ, et al. (1997) Crystal structure of the complex between human CD8alpha(alpha) and HLA-A2. Nature 387: 630-634.
    • (1997) Nature , vol.387 , pp. 630-634
    • Gao, G.F.1    Tormo, J.2    Gerth, U.C.3    Wyer, J.R.4    McMichael, A.J.5
  • 6
    • 30744455459 scopus 로고    scopus 로고
    • Structural prediction of peptides bound to MHC class I
    • Fagerberg T, Cerottini J-C, Michielin O, (2006) Structural prediction of peptides bound to MHC class I. J Mol Biol. 356: 521-546.
    • (2006) J Mol Biol , vol.356 , pp. 521-546
    • Fagerberg, T.1    Cerottini, J.-C.2    Michielin, O.3
  • 8
    • 0032387825 scopus 로고    scopus 로고
    • Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models
    • Mamitsuka H, (1998) Predicting peptides that bind to MHC molecules using supervised learning of hidden Markov models. Proteins 33: 460-474.
    • (1998) Proteins , vol.33 , pp. 460-474
    • Mamitsuka, H.1
  • 9
    • 2942524864 scopus 로고
    • Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis
    • Sette A, Buus S, Appella E, Smith JA, Chesnut R, et al. (1989) Prediction of major histocompatibility complex binding regions of protein antigens by sequence pattern analysis. Proc Natl Acad Sci U S A 86: 3296-3300.
    • (1989) Proc Natl Acad Sci U S A , vol.86 , pp. 3296-3300
    • Sette, A.1    Buus, S.2    Appella, E.3    Smith, J.A.4    Chesnut, R.5
  • 10
    • 0025855156 scopus 로고
    • Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules
    • Falk K, Rotzschke O, Stevanovic S, Jung G, Rammensee HG, (1991) Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules. Nature 351: 290-296.
    • (1991) Nature , vol.351 , pp. 290-296
    • Falk, K.1    Rotzschke, O.2    Stevanovic, S.3    Jung, G.4    Rammensee, H.G.5
  • 11
    • 0028052724 scopus 로고
    • Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains
    • Parker KC, Bednarek MA, Coligan JE, (1994) Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol 152: 163-175.
    • (1994) J Immunol , vol.152 , pp. 163-175
    • Parker, K.C.1    Bednarek, M.A.2    Coligan, J.E.3
  • 12
    • 0029125234 scopus 로고
    • An empirical method for the prediction of T-cell epitopes
    • Davenport MP, Ho Shon IA, Hill AV, (1995) An empirical method for the prediction of T-cell epitopes. Immunogenetics 42: 392-397.
    • (1995) Immunogenetics , vol.42 , pp. 392-397
    • Davenport, M.P.1    Ho Shon, I.A.2    Hill, A.V.3
  • 14
    • 0035989339 scopus 로고    scopus 로고
    • Prediction of promiscuous peptides that bind HLA class I molecules
    • Brusic V, Petrovsky N, Zhang G, Bajic VB, (2002) Prediction of promiscuous peptides that bind HLA class I molecules. Immunol Cell Biol 80: 280-285.
    • (2002) Immunol Cell Biol , vol.80 , pp. 280-285
    • Brusic, V.1    Petrovsky, N.2    Zhang, G.3    Bajic, V.B.4
  • 16
    • 42549105195 scopus 로고    scopus 로고
    • Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research
    • Lin HH, Ray S, Tongchusak S, Reinherz EL, Brusic V, (2008) Evaluation of MHC class I peptide binding prediction servers: applications for vaccine research. BMC Immunol 9: 8.
    • (2008) BMC Immunol , vol.9 , pp. 8
    • Lin, H.H.1    Ray, S.2    Tongchusak, S.3    Reinherz, E.L.4    Brusic, V.5
  • 17
    • 0037407113 scopus 로고    scopus 로고
    • Reliable prediction of T-cell epitopes using neural networks with novel sequence representations
    • Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, et al. (2003) Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12: 1007-1017.
    • (2003) Protein Sci , vol.12 , pp. 1007-1017
    • Nielsen, M.1    Lundegaard, C.2    Worning, P.3    Lauemoller, S.L.4    Lamberth, K.5
  • 18
    • 33947505235 scopus 로고    scopus 로고
    • A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes
    • Bhasin M, Raghava GP, (2007) A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. J Biosci 32: 31-42.
    • (2007) J Biosci , vol.32 , pp. 31-42
    • Bhasin, M.1    Raghava, G.P.2
  • 19
    • 33746218584 scopus 로고    scopus 로고
    • MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties
    • Cui J, Han LY, Lin HH, Tang ZQ, Jiang L, et al. (2006) MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties. Immunogenetics 58: 607-613.
    • (2006) Immunogenetics , vol.58 , pp. 607-613
    • Cui, J.1    Han, L.Y.2    Lin, H.H.3    Tang, Z.Q.4    Jiang, L.5
  • 20
    • 33847710294 scopus 로고    scopus 로고
    • Prediction of supertype-specific HLA class I binding peptides using support vector machines
    • Zhang GL, Bozic I, Kwoh CK, August JT, Brusic V, (2007) Prediction of supertype-specific HLA class I binding peptides using support vector machines. J Immunol Methods 320: 143-154.
    • (2007) J Immunol Methods , vol.320 , pp. 143-154
    • Zhang, G.L.1    Bozic, I.2    Kwoh, C.K.3    August, J.T.4    Brusic, V.5
  • 21
    • 38849139819 scopus 로고    scopus 로고
    • Efficient peptide-MHC-I binding prediction for alleles with few known binders
    • Jacob L, Vert JP, (2008) Efficient peptide-MHC-I binding prediction for alleles with few known binders. Bioinformatics 24: 358-366.
    • (2008) Bioinformatics , vol.24 , pp. 358-366
    • Jacob, L.1    Vert, J.P.2
  • 23
    • 4344589929 scopus 로고    scopus 로고
    • Modeling the structure of bound peptide ligands to major histocompatibility complex
    • Tong JC, Tan TW, Ranganathan S, (2004) Modeling the structure of bound peptide ligands to major histocompatibility complex. Protein Sci 13: 2523-2532.
    • (2004) Protein Sci , vol.13 , pp. 2523-2532
    • Tong, J.C.1    Tan, T.W.2    Ranganathan, S.3
  • 24
    • 79957628239 scopus 로고    scopus 로고
    • Predicting peptide binding to Major Histocompatibility Complex molecules
    • Liao WW, Arthur JW, (2011) Predicting peptide binding to Major Histocompatibility Complex molecules. Autoimmun Rev 10: 469-473.
    • (2011) Autoimmun Rev , vol.10 , pp. 469-473
    • Liao, W.W.1    Arthur, J.W.2
  • 26
    • 0033523959 scopus 로고    scopus 로고
    • Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins
    • Rognan D, Lauemoller SL, Holm A, Buus S, Tschinke V, (1999) Predicting binding affinities of protein ligands from three-dimensional models: application to peptide binding to class I major histocompatibility proteins. J Med Chem 42: 4650-4658.
    • (1999) J Med Chem , vol.42 , pp. 4650-4658
    • Rognan, D.1    Lauemoller, S.L.2    Holm, A.3    Buus, S.4    Tschinke, V.5
  • 27
    • 0036447407 scopus 로고    scopus 로고
    • Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis
    • Michielin O, Karplus M, (2002) Binding free energy differences in a TCR-peptide-MHC complex induced by a peptide mutation: a simulation analysis. J Mol Biol 324: 547-569.
    • (2002) J Mol Biol , vol.324 , pp. 547-569
    • Michielin, O.1    Karplus, M.2
  • 28
    • 34547599808 scopus 로고    scopus 로고
    • MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes
    • Kumar N, Mohanty D, (2007) MODPROPEP: a program for knowledge-based modeling of protein-peptide complexes. Nucleic Acids Res 35: W549-555.
    • (2007) Nucleic Acids Res , vol.35
    • Kumar, N.1    Mohanty, D.2
  • 29
    • 80053066016 scopus 로고    scopus 로고
    • Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function
    • Liao WW, Arthur JW, (2011) Predicting peptide binding affinities to MHC molecules using a modified semi-empirical scoring function. PLoS One 6: e25055.
    • (2011) PLoS One , vol.6
    • Liao, W.W.1    Arthur, J.W.2
  • 30
    • 0029018773 scopus 로고
    • Ranking potential binding peptides to MHC molecules by a computational threading approach
    • Altuvia Y, Schueler O, Margalit H, (1995) Ranking potential binding peptides to MHC molecules by a computational threading approach. J Mol Biol 249: 244-250.
    • (1995) J Mol Biol , vol.249 , pp. 244-250
    • Altuvia, Y.1    Schueler, O.2    Margalit, H.3
  • 32
    • 7944235990 scopus 로고    scopus 로고
    • A structure-based approach for prediction of MHC-binding peptides
    • Altuvia Y, Margalit H, (2004) A structure-based approach for prediction of MHC-binding peptides. Methods 34: 454-459.
    • (2004) Methods , vol.34 , pp. 454-459
    • Altuvia, Y.1    Margalit, H.2
  • 33
    • 0036554917 scopus 로고    scopus 로고
    • Recovery of known T-cell epitopes by computational scanning of a viral genome
    • Logean A, Rognan D, (2002) Recovery of known T-cell epitopes by computational scanning of a viral genome. J Comput Aided Mol Des 16: 229-243.
    • (2002) J Comput Aided Mol Des , vol.16 , pp. 229-243
    • Logean, A.1    Rognan, D.2
  • 34
    • 33645034411 scopus 로고    scopus 로고
    • Structural prediction of peptides binding to MHC class I molecules
    • Bui H-H, Schiewe AJ, von Grafenstein H, Haworth IS, (2006) Structural prediction of peptides binding to MHC class I molecules. Proteins 63: 43-52.
    • (2006) Proteins , vol.63 , pp. 43-52
    • Bui, H.-H.1    Schiewe, A.J.2    von Grafenstein, H.3    Haworth, I.S.4
  • 35
    • 7944229323 scopus 로고    scopus 로고
    • Quantitative structure-activity relationships and the prediction of MHC supermotifs
    • Doytchinova IA, Guan P, Flower DR, (2004) Quantitative structure-activity relationships and the prediction of MHC supermotifs. Methods 34: 444-453.
    • (2004) Methods , vol.34 , pp. 444-453
    • Doytchinova, I.A.1    Guan, P.2    Flower, D.R.3
  • 36
    • 44649192502 scopus 로고    scopus 로고
    • Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships
    • Hattotuwagama CK, Doytchinova IA, Flower DR, (2007) Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity: in silico bioinformatic step-by-step guide using quantitative structure-activity relationships. Methods Mol Biol 409: 227-245.
    • (2007) Methods Mol Biol , vol.409 , pp. 227-245
    • Hattotuwagama, C.K.1    Doytchinova, I.A.2    Flower, D.R.3
  • 37
    • 0029926327 scopus 로고    scopus 로고
    • Selection of peptides that bind to the HLA-A2.1 molecule by molecular modelling
    • Lim JS, Kim S, Lee HG, Lee KY, Kwon TJ, et al. (1996) Selection of peptides that bind to the HLA-A2.1 molecule by molecular modelling. Mol Immunol 33: 221-230.
    • (1996) Mol Immunol , vol.33 , pp. 221-230
    • Lim, J.S.1    Kim, S.2    Lee, H.G.3    Lee, K.Y.4    Kwon, T.J.5
  • 38
    • 33646058599 scopus 로고    scopus 로고
    • Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes
    • Bordner AJ, Abagyan R, (2006) Ab initio prediction of peptide-MHC binding geometry for diverse class I MHC allotypes. Proteins 63: 512-526.
    • (2006) Proteins , vol.63 , pp. 512-526
    • Bordner, A.J.1    Abagyan, R.2
  • 39
    • 78149445777 scopus 로고    scopus 로고
    • Structure-based identification of MHC binding peptides: Benchmarking of prediction accuracy
    • Kumar N, Mohanty D, (2010) Structure-based identification of MHC binding peptides: Benchmarking of prediction accuracy. Mol Biosyst 6: 2508-2520.
    • (2010) Mol Biosyst , vol.6 , pp. 2508-2520
    • Kumar, N.1    Mohanty, D.2
  • 40
    • 0026618817 scopus 로고
    • Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle
    • Guo HC, Jardetzky TS, Garrett TP, Lane WS, Strominger JL, et al. (1992) Different length peptides bind to HLA-Aw68 similarly at their ends but bulge out in the middle. Nature 360: 364-366.
    • (1992) Nature , vol.360 , pp. 364-366
    • Guo, H.C.1    Jardetzky, T.S.2    Garrett, T.P.3    Lane, W.S.4    Strominger, J.L.5
  • 41
    • 70450106216 scopus 로고    scopus 로고
    • Improved prediction of protein side-chain conformations with SCWRL4
    • Krivov GG, Shapovalov MV, Dunbrack J, Roland L, (2009) Improved prediction of protein side-chain conformations with SCWRL4. Proteins 77: 778-795.
    • (2009) Proteins , vol.77 , pp. 778-795
    • Krivov, G.G.1    Shapovalov, M.V.2    Dunbrack, J.3    Roland, L.4
  • 42
    • 33745584371 scopus 로고    scopus 로고
    • A community resource benchmarking predictions of peptide binding to MHC-I molecules
    • Peters B, Bui H-H, Frankild S, Nielson M, Lundegaard C, et al. (2006) A community resource benchmarking predictions of peptide binding to MHC-I molecules. PLoS Comput Biol 2: e65.
    • (2006) PLoS Comput Biol , vol.2
    • Peters, B.1    Bui, H.-H.2    Frankild, S.3    Nielson, M.4    Lundegaard, C.5
  • 43
    • 41949142649 scopus 로고    scopus 로고
    • Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
    • Zhang GL, Khan AM, Srinivasan KN, Heiny A, Lee K, et al. (2008) Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. BMC Bioinformatics 9 Suppl 1: S19.
    • (2008) BMC Bioinformatics , vol.9
    • Zhang, G.L.1    Khan, A.M.2    Srinivasan, K.N.3    Heiny, A.4    Lee, K.5
  • 44
    • 39049111013 scopus 로고    scopus 로고
    • Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain
    • Hou T, Zhang W, Case DA, Wang W, (2008) Characterization of domain-peptide interaction interface: a case study on the amphiphysin-1 SH3 domain. J Mol Biol 376: 1201-1214.
    • (2008) J Mol Biol , vol.376 , pp. 1201-1214
    • Hou, T.1    Zhang, W.2    Case, D.A.3    Wang, W.4
  • 45
    • 0035892137 scopus 로고    scopus 로고
    • Bone marrow transplantation from unrelated donors: the impact of mismatches with substitutions at position 116 of the human leukocyte antigen class I heavy chain
    • Ferrara GB, Bacigalupo A, Lamparelli T, Lanino E, Delfino L, et al. (2001) Bone marrow transplantation from unrelated donors: the impact of mismatches with substitutions at position 116 of the human leukocyte antigen class I heavy chain. Blood 98: 3150-3155.
    • (2001) Blood , vol.98 , pp. 3150-3155
    • Ferrara, G.B.1    Bacigalupo, A.2    Lamparelli, T.3    Lanino, E.4    Delfino, L.5
  • 46
    • 63849288804 scopus 로고    scopus 로고
    • HLA mismatch combinations associated with decreased risk of relapse: implications for the molecular mechanism
    • Kawase T, Matsuo K, Kashiwase K, Inoko H, Saji H, et al. (2009) HLA mismatch combinations associated with decreased risk of relapse: implications for the molecular mechanism. Blood 113: 2851-2858.
    • (2009) Blood , vol.113 , pp. 2851-2858
    • Kawase, T.1    Matsuo, K.2    Kashiwase, K.3    Inoko, H.4    Saji, H.5
  • 47
    • 34948865802 scopus 로고    scopus 로고
    • High-risk HLA allele mismatch combinations responsible for severe acute graft-versus-host disease and implication for its molecular mechanism
    • Kawase T, Morishima Y, Matsuo K, Kashiwase K, Inoko H, et al. (2007) High-risk HLA allele mismatch combinations responsible for severe acute graft-versus-host disease and implication for its molecular mechanism. Blood 110: 2235-2241.
    • (2007) Blood , vol.110 , pp. 2235-2241
    • Kawase, T.1    Morishima, Y.2    Matsuo, K.3    Kashiwase, K.4    Inoko, H.5
  • 48
    • 84857033887 scopus 로고    scopus 로고
    • Identification by random forest method of HLA class I amino acid substitutions associated with lower survival at day 100 in unrelated donor hematopoietic cell transplantation
    • Marino SR, Lin S, Maiers M, Haagenson M, Spellman S, et al. (2012) Identification by random forest method of HLA class I amino acid substitutions associated with lower survival at day 100 in unrelated donor hematopoietic cell transplantation. Bone Marrow Transplant 47: 217-226.
    • (2012) Bone Marrow Transplant , vol.47 , pp. 217-226
    • Marino, S.R.1    Lin, S.2    Maiers, M.3    Haagenson, M.4    Spellman, S.5
  • 49
    • 76649121529 scopus 로고    scopus 로고
    • MM-GBSA binding free energy decomposition and T cell receptor engineering
    • Zoete V, Irving MB, Michielin O, (2010) MM-GBSA binding free energy decomposition and T cell receptor engineering. J Mol Recognit 23: 142-152.
    • (2010) J Mol Recognit , vol.23 , pp. 142-152
    • Zoete, V.1    Irving, M.B.2    Michielin, O.3
  • 50
    • 41149150251 scopus 로고    scopus 로고
    • Water: water-an enduring mystery
    • Ball P, (2008) Water: water-an enduring mystery. Nature 452: 291-292.
    • (2008) Nature , vol.452 , pp. 291-292
    • Ball, P.1
  • 51
    • 78650214391 scopus 로고    scopus 로고
    • Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex
    • García-Sosa AT, Mancera RL, (2010) Free Energy Calculations of Mutations Involving a Tightly Bound Water Molecule and Ligand Substitutions in a Ligand-Protein Complex. Molecular Informatics 29: 589.
    • (2010) Molecular Informatics , vol.29 , pp. 589
    • García-Sosa, A.T.1    Mancera, R.L.2
  • 52
    • 77953955973 scopus 로고    scopus 로고
    • A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity
    • Luo W, Pei J, Zhu Y, (2010) A fast protein-ligand docking algorithm based on hydrogen bond matching and surface shape complementarity. J Mol Model 16: 903-913.
    • (2010) J Mol Model , vol.16 , pp. 903-913
    • Luo, W.1    Pei, J.2    Zhu, Y.3
  • 55
    • 0025008168 scopus 로고
    • Sequence logos: a new way to display consensus sequences
    • Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100.
    • (1990) Nucleic Acids Res , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2


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