메뉴 건너뛰기




Volumn 14, Issue SUPPL4, 2013, Pages

Prediction of conformational epitopes with the use of a knowledge-based energy function and geometrically related neighboring residue characteristics

Author keywords

[No Author keywords available]

Indexed keywords

10-FOLD CROSS-VALIDATION; AMINO ACID RESIDUES; B-CELL RECEPTORS; CONFORMATIONAL EPITOPES; ENERGY FUNCTIONS; MORPHOLOGICAL ALGORITHMS; SURFACE RESIDUES; SYNTHETIC VACCINES;

EID: 84879511692     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-S4-S3     Document Type: Article
Times cited : (30)

References (36)
  • 1
    • 64049090391 scopus 로고    scopus 로고
    • An introduction to epitope prediction methods and software
    • 10.1002/rmv.602, 19101924
    • Yang X, Yu X. An introduction to epitope prediction methods and software. Rev Med Virol 2009, 19(2):77-96. 10.1002/rmv.602, 19101924.
    • (2009) Rev Med Virol , vol.19 , Issue.2 , pp. 77-96
    • Yang, X.1    Yu, X.2
  • 2
    • 0032875696 scopus 로고    scopus 로고
    • Defining epitopes: It's not as easy as it seems
    • 10.1038/13590, 10504677
    • Greenspan NS, Di Cera E. Defining epitopes: It's not as easy as it seems. Nat Biotechnol 1999, 17(10):936-937. 10.1038/13590, 10504677.
    • (1999) Nat Biotechnol , vol.17 , Issue.10 , pp. 936-937
    • Greenspan, N.S.1    Di Cera, E.2
  • 3
    • 84869234333 scopus 로고    scopus 로고
    • Longitudinal analysis of the human antibody response to chikungunya virus infection: implications for sero-diagnosis assays and vaccine development
    • Kam YW, Lee WW, Simarmata D, Harjanto S, Teng TS, Tolou H, Chow A, Lin RT, Leo YS, Renia L, et al. Longitudinal analysis of the human antibody response to chikungunya virus infection: implications for sero-diagnosis assays and vaccine development. J Virol 2012,
    • (2012) J Virol
    • Kam, Y.W.1    Lee, W.W.2    Simarmata, D.3    Harjanto, S.4    Teng, T.S.5    Tolou, H.6    Chow, A.7    Lin, R.T.8    Leo, Y.S.9    Renia, L.10
  • 4
    • 84886844561 scopus 로고    scopus 로고
    • The use of epitope arrays in immuno-diagnosis of infectious disease: HCV a case study
    • Siman-Tov DD, Zemel R, Kaspa RT, Gershoni JM. The use of epitope arrays in immuno-diagnosis of infectious disease: HCV a case study. Anal Biochem 2012,
    • (2012) Anal Biochem
    • Siman-Tov, D.D.1    Zemel, R.2    Kaspa, R.T.3    Gershoni, J.M.4
  • 6
    • 0022555298 scopus 로고
    • Structural basis for antigen-antibody recognition
    • 10.1126/science.2426777, 2426777
    • Huber R. Structural basis for antigen-antibody recognition. Science 1986, 233(4765):702-703. 10.1126/science.2426777, 2426777.
    • (1986) Science , vol.233 , Issue.4765 , pp. 702-703
    • Huber, R.1
  • 7
    • 0035699903 scopus 로고    scopus 로고
    • Antigenicity and immunogenicity of synthetic peptides
    • 10.1006/biol.2001.0308, 11851317
    • Van Regenmortel MH. Antigenicity and immunogenicity of synthetic peptides. Biologicals 2001, 29(3-4):209-213. 10.1006/biol.2001.0308, 11851317.
    • (2001) Biologicals , vol.29 , Issue.3-4 , pp. 209-213
    • Van Regenmortel, M.H.1
  • 8
    • 0037263777 scopus 로고    scopus 로고
    • BEPITOPE: predicting the location of continuous epitopes and patterns in proteins
    • 10.1002/jmr.602, 12557235
    • Odorico M, Pellequer JL. BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit 2003, 16(1):20-22. 10.1002/jmr.602, 12557235.
    • (2003) J Mol Recognit , vol.16 , Issue.1 , pp. 20-22
    • Odorico, M.1    Pellequer, J.L.2
  • 9
    • 35048872790 scopus 로고    scopus 로고
    • BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physical-chemical properties
    • Saha S, Raghava GPS. BcePred: Prediction of continuous B-cell epitopes in antigenic sequences using physical-chemical properties. LNCS 2004, 3239:197-204.
    • (2004) LNCS , vol.3239 , pp. 197-204
    • Saha, S.1    Raghava, G.P.S.2
  • 10
    • 33751104704 scopus 로고    scopus 로고
    • Improved method for predicting linear B-cell epitopes
    • 10.1186/1745-7580-2-2, 1479323, 16635264
    • Larsen JE, Lund O, Nielsen M. Improved method for predicting linear B-cell epitopes. Immunome Res 2006, 2:2. 10.1186/1745-7580-2-2, 1479323, 16635264.
    • (2006) Immunome Res , vol.2 , pp. 2
    • Larsen, J.E.1    Lund, O.2    Nielsen, M.3
  • 11
    • 33748254730 scopus 로고    scopus 로고
    • Prediction of continuous B-cell epitopes in an antigen using recurrent neural network
    • 10.1002/prot.21078, 16894596
    • Saha S, Raghava GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 2006, 65(1):40-48. 10.1002/prot.21078, 16894596.
    • (2006) Proteins , vol.65 , Issue.1 , pp. 40-48
    • Saha, S.1    Raghava, G.P.2
  • 12
    • 56749156105 scopus 로고    scopus 로고
    • Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches
    • 10.1002/jmr.910, 18680207
    • Chang HT, Liu CH, Pai TW. Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches. J Mol Recognit 2008, 21(6):431-441. 10.1002/jmr.910, 18680207.
    • (2008) J Mol Recognit , vol.21 , Issue.6 , pp. 431-441
    • Chang, H.T.1    Liu, C.H.2    Pai, T.W.3
  • 13
    • 80053513645 scopus 로고    scopus 로고
    • Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification
    • 3163029, 21876642
    • Wang HW, Lin YC, Pai TW, Chang HT. Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J Biomed Biotechnol 2011, 2011:432830. 3163029, 21876642.
    • (2011) J Biomed Biotechnol , vol.2011 , pp. 432830
    • Wang, H.W.1    Lin, Y.C.2    Pai, T.W.3    Chang, H.T.4
  • 14
    • 47649130438 scopus 로고    scopus 로고
    • Predicting linear B-cell epitopes using string kernels
    • 10.1002/jmr.893, 2683948, 18496882
    • El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit 2008, 21(4):243-255. 10.1002/jmr.893, 2683948, 18496882.
    • (2008) J Mol Recognit , vol.21 , Issue.4 , pp. 243-255
    • El-Manzalawy, Y.1    Dobbs, D.2    Honavar, V.3
  • 15
    • 0030174309 scopus 로고    scopus 로고
    • Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity
    • 10.1006/meth.1996.0054, 8812702
    • Van Regenmortel MHV. Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity. Methods 1996, 9(3):465-472. 10.1006/meth.1996.0054, 8812702.
    • (1996) Methods , vol.9 , Issue.3 , pp. 465-472
    • Van Regenmortel, M.H.V.1
  • 16
    • 23144457577 scopus 로고    scopus 로고
    • CEP: a conformational epitope prediction server
    • Web Server, 10.1093/nar/gki460, 1160221, 15980448
    • Kulkarni-Kale U, Bhosle S, Kolaskar AS. CEP: a conformational epitope prediction server. Nucleic Acids Res 2005, 33(Web Server):W168-171. 10.1093/nar/gki460, 1160221, 15980448.
    • (2005) Nucleic Acids Res , vol.33
    • Kulkarni-Kale, U.1    Bhosle, S.2    Kolaskar, A.S.3
  • 17
    • 33751099863 scopus 로고    scopus 로고
    • Prediction of residues in discontinuous B-cell epitopes using protein 3D structures
    • 10.1110/ps.062405906, 2242418, 17001032
    • Haste Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 2006, 15(11):2558-2567. 10.1110/ps.062405906, 2242418, 17001032.
    • (2006) Protein Sci , vol.15 , Issue.11 , pp. 2558-2567
    • Haste Andersen, P.1    Nielsen, M.2    Lund, O.3
  • 19
    • 58049187138 scopus 로고    scopus 로고
    • ElliPro: a new structure-based tool for the prediction of antibody epitopes
    • 10.1186/1471-2105-9-514, 2607291, 19055730
    • Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 2008, 9:514. 10.1186/1471-2105-9-514, 2607291, 19055730.
    • (2008) BMC Bioinformatics , vol.9 , pp. 514
    • Ponomarenko, J.1    Bui, H.H.2    Li, W.3    Fusseder, N.4    Bourne, P.E.5    Sette, A.6    Peters, B.7
  • 20
    • 45449086674 scopus 로고    scopus 로고
    • PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure
    • 10.1093/bioinformatics/btn199, 18443018
    • Sweredoski MJ, Baldi P. PEPITO: improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure. Bioinformatics 2008, 24(12):1459-1460. 10.1093/bioinformatics/btn199, 18443018.
    • (2008) Bioinformatics , vol.24 , Issue.12 , pp. 1459-1460
    • Sweredoski, M.J.1    Baldi, P.2
  • 21
    • 67849086859 scopus 로고    scopus 로고
    • SEPPA: a computational server for spatial epitope prediction of protein antigens
    • Web Server, 10.1093/nar/gkp417, 2703964, 19465377
    • Sun J, Wu D, Xu T, Wang X, Xu X, Tao L, Li YX, Cao ZW. SEPPA: a computational server for spatial epitope prediction of protein antigens. Nucleic Acids Res 2009, 37(Web Server):W612-616. 10.1093/nar/gkp417, 2703964, 19465377.
    • (2009) Nucleic Acids Res , vol.37
    • Sun, J.1    Wu, D.2    Xu, T.3    Wang, X.4    Xu, X.5    Tao, L.6    Li, Y.X.7    Cao, Z.W.8
  • 22
    • 33646150213 scopus 로고    scopus 로고
    • Discontinuous epitope prediction based on mimotope analysis
    • 10.1093/bioinformatics/btl012, 16434442
    • Moreau V, Granier C, Villard S, Laune D, Molina F. Discontinuous epitope prediction based on mimotope analysis. Bioinformatics 2006, 22(9):1088-1095. 10.1093/bioinformatics/btl012, 16434442.
    • (2006) Bioinformatics , vol.22 , Issue.9 , pp. 1088-1095
    • Moreau, V.1    Granier, C.2    Villard, S.3    Laune, D.4    Molina, F.5
  • 23
    • 34249886331 scopus 로고    scopus 로고
    • Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm
    • 10.1002/prot.21387, 17427229
    • Bublil EM, Freund NT, Mayrose I, Penn O, Roitburd-Berman A, Rubinstein ND, Pupko T, Gershoni JM. Stepwise prediction of conformational discontinuous B-cell epitopes using the Mapitope algorithm. Proteins 2007, 68(1):294-304. 10.1002/prot.21387, 17427229.
    • (2007) Proteins , vol.68 , Issue.1 , pp. 294-304
    • Bublil, E.M.1    Freund, N.T.2    Mayrose, I.3    Penn, O.4    Roitburd-Berman, A.5    Rubinstein, N.D.6    Pupko, T.7    Gershoni, J.M.8
  • 24
    • 60649084396 scopus 로고    scopus 로고
    • Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis
    • 10.1186/1471-2105-9-538, 2639436, 19087303
    • Huang YX, Bao YL, Guo SY, Wang Y, Zhou CG, Li YX. Pep-3D-Search: a method for B-cell epitope prediction based on mimotope analysis. BMC Bioinformatics 2008, 9:538. 10.1186/1471-2105-9-538, 2639436, 19087303.
    • (2008) BMC Bioinformatics , vol.9 , pp. 538
    • Huang, Y.X.1    Bao, Y.L.2    Guo, S.Y.3    Wang, Y.4    Zhou, C.G.5    Li, Y.X.6
  • 25
    • 0030043489 scopus 로고    scopus 로고
    • Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp
    • 10.1126/science.271.5246.163, 8539615
    • Dougherty DA. Cation-pi interactions in chemistry and biology: a new view of benzene, Phe, Tyr, and Trp. Science 1996, 271(5246):163-168. 10.1126/science.271.5246.163, 8539615.
    • (1996) Science , vol.271 , Issue.5246 , pp. 163-168
    • Dougherty, D.A.1
  • 26
    • 0024362070 scopus 로고
    • On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5
    • 10.1021/bi00437a034, 2475171
    • Novotny J, Bruccoleri RE, Saul FA. On the attribution of binding energy in antigen-antibody complexes McPC 603, D1.3, and HyHEL-5. Biochemistry 1989, 28(11):4735-4749. 10.1021/bi00437a034, 2475171.
    • (1989) Biochemistry , vol.28 , Issue.11 , pp. 4735-4749
    • Novotny, J.1    Bruccoleri, R.E.2    Saul, F.A.3
  • 27
    • 0035882533 scopus 로고    scopus 로고
    • A distance-dependent atomic knowledge-based potential for improved protein structure selection
    • 10.1002/prot.1087, 11455595
    • Lu H, Skolnick J. A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 2001, 44(3):223-232. 10.1002/prot.1087, 11455595.
    • (2001) Proteins , vol.44 , Issue.3 , pp. 223-232
    • Lu, H.1    Skolnick, J.2
  • 28
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Web Server, 10.1093/nar/gkm290, 1933241, 17517781
    • Wiederstein M, Sippl MJ. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 2007, 35(Web Server):W407-410. 10.1093/nar/gkm290, 1933241, 17517781.
    • (2007) Nucleic Acids Res , vol.35
    • Wiederstein, M.1    Sippl, M.J.2
  • 29
    • 34548301416 scopus 로고    scopus 로고
    • Prediction of linear B-cell epitopes using amino acid pair antigenicity scale
    • 10.1007/s00726-006-0485-9, 17252308
    • Chen J, Liu H, Yang J, Chou KC. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 2007, 33(3):423-428. 10.1007/s00726-006-0485-9, 17252308.
    • (2007) Amino Acids , vol.33 , Issue.3 , pp. 423-428
    • Chen, J.1    Liu, H.2    Yang, J.3    Chou, K.C.4
  • 31
    • 0021107965 scopus 로고
    • Solvent-accessible surfaces of proteins and nucleic acids
    • 10.1126/science.6879170, 6879170
    • Connolly ML. Solvent-accessible surfaces of proteins and nucleic acids. Science 1983, 221(4612):709-713. 10.1126/science.6879170, 6879170.
    • (1983) Science , vol.221 , Issue.4612 , pp. 709-713
    • Connolly, M.L.1
  • 32
    • 0036171255 scopus 로고    scopus 로고
    • SACS--self-maintaining database of antibody crystal structure information
    • 10.1093/bioinformatics/18.1.175, 11836226
    • Allcorn LC, Martin AC. SACS--self-maintaining database of antibody crystal structure information. Bioinformatics 2002, 18(1):175-181. 10.1093/bioinformatics/18.1.175, 11836226.
    • (2002) Bioinformatics , vol.18 , Issue.1 , pp. 175-181
    • Allcorn, L.C.1    Martin, A.C.2
  • 33
    • 0015222647 scopus 로고
    • The interpretation of protein structures: estimation of static accessibility
    • 10.1016/0022-2836(71)90324-X, 5551392
    • Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971, 55(3):379-400. 10.1016/0022-2836(71)90324-X, 5551392.
    • (1971) J Mol Biol , vol.55 , Issue.3 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 34
    • 0017429069 scopus 로고
    • Areas, volumes, packing and protein structure
    • 10.1146/annurev.bb.06.060177.001055, 326146
    • Richards FM. Areas, volumes, packing and protein structure. Annu Rev Biophys Bioeng 1977, 6:151-176. 10.1146/annurev.bb.06.060177.001055, 326146.
    • (1977) Annu Rev Biophys Bioeng , vol.6 , pp. 151-176
    • Richards, F.M.1
  • 35
    • 33744986320 scopus 로고    scopus 로고
    • The family 21 carbohydrate-binding module of glucoamylase from Rhizopus oryzae consists of two sites playing distinct roles in ligand binding
    • 10.1042/BJ20051982, 1482813, 16509822
    • Chou WI, Pai TW, Liu SH, Hsiung BK, Chang MD. The family 21 carbohydrate-binding module of glucoamylase from Rhizopus oryzae consists of two sites playing distinct roles in ligand binding. Biochem J 2006, 396(3):469-477. 10.1042/BJ20051982, 1482813, 16509822.
    • (2006) Biochem J , vol.396 , Issue.3 , pp. 469-477
    • Chou, W.I.1    Pai, T.W.2    Liu, S.H.3    Hsiung, B.K.4    Chang, M.D.5
  • 36
    • 0038076054 scopus 로고    scopus 로고
    • X-ray structure of a voltage-dependent K+ channel
    • 10.1038/nature01580, 12721618
    • Jiang Y, Lee A, Chen J, Ruta V, Cadene M, Chait BT, MacKinnon R. X-ray structure of a voltage-dependent K+ channel. Nature 2003, 423(6935):33-41. 10.1038/nature01580, 12721618.
    • (2003) Nature , vol.423 , Issue.6935 , pp. 33-41
    • Jiang, Y.1    Lee, A.2    Chen, J.3    Ruta, V.4    Cadene, M.5    Chait, B.T.6    MacKinnon, R.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.