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Volumn 37, Issue SUPPL. 2, 2009, Pages

RosettaAntibody: Antibody variable region homology modeling server

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY;

EID: 67849111558     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp387     Document Type: Article
Times cited : (131)

References (50)
  • 1
    • 33644839662 scopus 로고    scopus 로고
    • Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis
    • Sivasubramanian,A., Chao,G., Pressler,H.M., Wittrup,K.D. and Gray,J.J. (2006) Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure, 14, 401-414.
    • (2006) Structure , vol.14 , pp. 401-414
    • Sivasubramanian, A.1    Chao, G.2    Pressler, H.M.3    Wittrup, K.D.4    Gray, J.J.5
  • 2
    • 37349109629 scopus 로고    scopus 로고
    • Modeling the structure of mAb 14B7 bound to the anthrax protective antigen
    • Sivasubramanian,A., Maynard,J.A. and Gray,J.J. (2008) Modeling the structure of mAb 14B7 bound to the anthrax protective antigen. Proteins, 70, 218-230.
    • (2008) Proteins , vol.70 , pp. 218-230
    • Sivasubramanian, A.1    Maynard, J.A.2    Gray, J.J.3
  • 3
    • 35148855712 scopus 로고    scopus 로고
    • Computational design of antibody-affinity improvement beyond in vivo maturation.n
    • Lippow,S.M., Wittrup,K.D. and Tidor,B. (2007) Computational design of antibody-affinity improvement beyond in vivo maturation.n Nat. Biotechnol., 25, 1171-1176.
    • (2007) Nat. Biotechnol , vol.25 , pp. 1171-1176
    • Lippow, S.M.1    Wittrup, K.D.2    Tidor, B.3
  • 5
    • 0034458999 scopus 로고    scopus 로고
    • WAM: An improved algorithm for modelling antibodies on the WEB
    • Whitelegg,N.R. and Rees,A.R. (2000) WAM: An improved algorithm for modelling antibodies on the WEB. Protein Eng., 13, 819-824.
    • (2000) Protein Eng , vol.13 , pp. 819-824
    • Whitelegg, N.R.1    Rees, A.R.2
  • 6
    • 50549090182 scopus 로고    scopus 로고
    • PIGS: Automatic prediction of antibody structures
    • Marcatili,P., Rosi,A. and Tramontano,A. (2008) PIGS: Automatic prediction of antibody structures. Bioinformatics, 24, 1953-1954.
    • (2008) Bioinformatics , vol.24 , pp. 1953-1954
    • Marcatili, P.1    Rosi, A.2    Tramontano, A.3
  • 7
    • 59449096415 scopus 로고    scopus 로고
    • Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
    • Sivasubramanian,A., Sircar,A., Chaudhury,S. and Gray,J.J. (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins, 74, 497-514.
    • (2009) Proteins , vol.74 , pp. 497-514
    • Sivasubramanian, A.1    Sircar, A.2    Chaudhury, S.3    Gray, J.J.4
  • 8
    • 50649095790 scopus 로고    scopus 로고
    • Macromolecular modeling with rosetta
    • Das,R. and Baker,D. (2008) Macromolecular modeling with rosetta. Annu. Rev. Biochem., 77, 363-382.
    • (2008) Annu. Rev. Biochem , vol.77 , pp. 363-382
    • Das, R.1    Baker, D.2
  • 9
    • 48449094112 scopus 로고    scopus 로고
    • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
    • Chaudhury,S. and Gray,J.J. (2008) Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J. Mol. Biol., 381, 1068-1087.
    • (2008) J. Mol. Biol , vol.381 , pp. 1068-1087
    • Chaudhury, S.1    Gray, J.J.2
  • 10
    • 0031585984 scopus 로고    scopus 로고
    • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions
    • Simons,K.T., Kooperberg,C., Huang,E. and Baker,D. (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J. Mol. Biol., 268, 209-225.
    • (1997) J. Mol. Biol , vol.268 , pp. 209-225
    • Simons, K.T.1    Kooperberg, C.2    Huang, E.3    Baker, D.4
  • 11
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • Canutescu,A.A. and Dunbrack,R.L. Jr. (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure. Potein Sci., 12 963-972.
    • (2003) Potein Sci , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 13
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang,C., Schueler-Furman,O. and Baker,D. (2005) Improved side-chain modeling for protein-protein docking. Protein Sci., 14, 1328-1339.
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 14
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme,T., Morozov,A.V. and Baker,D. (2003) An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326, 1239-1259.
    • (2003) J. Mol. Biol , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 15
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis,T. and Karplus,M. (1999) Effective energy function for proteins in solution. Proteins, 35, 133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 16
    • 1842326139 scopus 로고    scopus 로고
    • Bayesian statistical analysis of protein side-chain rotamer preferences
    • Dunbrack,R.L. Jr. and Cohen,F.E. (1997) Bayesian statistical analysis of protein side-chain rotamer preferences. Protein Sci., 6, 1661-1681.
    • (1997) Protein Sci , vol.6 , pp. 1661-1681
    • Dunbrack Jr., R.L.1    Cohen, F.E.2
  • 17
    • 0021480222 scopus 로고
    • Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability
    • Warshel,A., Russell,S.T. and Churg,A.K. (1984) Macroscopic models for studies of electrostatic interactions in proteins: Limitations and applicability. Proc. Natl Acad. Sci. USA, 81, 4785-4789.
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , pp. 4785-4789
    • Warshel, A.1    Russell, S.T.2    Churg, A.K.3
  • 19
    • 0031558798 scopus 로고    scopus 로고
    • Standard conformations for the canonical structures of immunoglobulins
    • Al-Lazikani,B., Lesk,A.M. and Chothia,C. (1997) Standard conformations for the canonical structures of immunoglobulins. J. Mol. Biol., 273, 927-948.
    • (1997) J. Mol. Biol , vol.273 , pp. 927-948
    • Al-Lazikani, B.1    Lesk, A.M.2    Chothia, C.3
  • 21
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez,R., Leplae,R., Lensink,M.F. and Wodak,S.J. (2005) Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins, 60, 150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 22
    • 60749123075 scopus 로고    scopus 로고
    • The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains
    • Honegger,A., Malebranche,A.D., Rothlisberger,D. and Pluckthun,A. (2009) The influence of the framework core residues on the biophysical properties of immunoglobulin heavy chain variable domains. Protein Eng. Des. Sel., 22, 121-134.
    • (2009) Protein Eng. Des. Sel , vol.22 , pp. 121-134
    • Honegger, A.1    Malebranche, A.D.2    Rothlisberger, D.3    Pluckthun, A.4
  • 24
    • 60749137123 scopus 로고    scopus 로고
    • Functional humanization of an anti-CD16 Fab fragment: Obstacles of switching from murine λ to human λ or κ light chains
    • Schlapschy,M., Fogarasi,M., Gruber,H., Gresch,O., Schafer,C., Aguib,Y. and Skerra,A. (2008) Functional humanization of an anti-CD16 Fab fragment: Obstacles of switching from murine λ to human λ or κ light chains. Protein Eng. Des. Sel., 22, 175-18.
    • (2008) Protein Eng. Des. Sel , vol.22 , pp. 175-218
    • Schlapschy, M.1    Fogarasi, M.2    Gruber, H.3    Gresch, O.4    Schafer, C.5    Aguib, Y.6    Skerra, A.7
  • 25
    • 0022558297 scopus 로고
    • Replacing the complementarity-determining regions in a human antibody with those from a mouse
    • Jones,P.T., Dear,P.H., Foote,J., Neuberger,M.S. and Winter,G. (1986) Replacing the complementarity-determining regions in a human antibody with those from a mouse. Nature, 321, 522-525.
    • (1986) Nature , vol.321 , pp. 522-525
    • Jones, P.T.1    Dear, P.H.2    Foote, J.3    Neuberger, M.S.4    Winter, G.5
  • 26
    • 37749042370 scopus 로고    scopus 로고
    • Antibody-protein interactions: Benchmark datasets and prediction tools evaluation
    • Ponomarenko,J.V. and Bourne,P.E. (2007) Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct. Biol. 7, 64.
    • (2007) BMC Struct. Biol , vol.7 , pp. 64
    • Ponomarenko, J.V.1    Bourne, P.E.2
  • 27
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray,J.J. (2006) High-resolution protein-protein docking. Curr. Opin. Struct. Biol., 16, 183-193.
    • (2006) Curr. Opin. Struct. Biol , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 28
    • 33846198406 scopus 로고    scopus 로고
    • Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP1(19) by computational docking
    • Autore,F., Melchiorre,S., Kleinjung,J., Morgan,W.D. and Fraternali,F. (2007) Interaction of malaria parasite-inhibitory antibodies with the merozoite surface protein MSP1(19) by computational docking. Proteins 66, 513-527.
    • (2007) Proteins , vol.66 , pp. 513-527
    • Autore, F.1    Melchiorre, S.2    Kleinjung, J.3    Morgan, W.D.4    Fraternali, F.5
  • 29
    • 0038302757 scopus 로고    scopus 로고
    • Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin
    • Bracci,L., Pini,A., Bernini,A., Lelli,B., Ricci,C., Scarselli,M., Niccolai,N. and Neri,P. (2003) Biochemical filtering of a protein-protein docking simulation identifies the structure of a complex between a recombinant antibody fragment and alpha-bungarotoxin. Biochem. J., 371, 423-427.
    • (2003) Biochem. J , vol.371 , pp. 423-427
    • Bracci, L.1    Pini, A.2    Bernini, A.3    Lelli, B.4    Ricci, C.5    Scarselli, M.6    Niccolai, N.7    Neri, P.8
  • 30
    • 35548990689 scopus 로고    scopus 로고
    • Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site
    • McKinney,B.A., Kallewaard,N.L., Crowe,J.E. Jr. and Meiler,J. (2007) Using the natural evolution of a rotavirus-specific human monoclonal antibody to predict the complex topography of a viral antigenic site. Immunome Res., 3, 8.
    • (2007) Immunome Res , vol.3 , pp. 8
    • McKinney, B.A.1    Kallewaard, N.L.2    Crowe Jr., J.E.3    Meiler, J.4
  • 31
    • 0345832301 scopus 로고    scopus 로고
    • ClusPro: An automated docking and discrimination method for the prediction of protein complexes
    • Comeau,S.R., Gatchell,D.W., Vajda,S. and Camacho,C.J. (2004) ClusPro: An automated docking and discrimination method for the prediction of protein complexes. Bioinformatics, 20, 45-50.
    • (2004) Bioinformatics , vol.20 , pp. 45-50
    • Comeau, S.R.1    Gatchell, D.W.2    Vajda, S.3    Camacho, C.J.4
  • 32
    • 33747840389 scopus 로고    scopus 로고
    • GRAMM-X public web server for protein-protein docking
    • Tovchigrechko,A. and Vakser,I.A. (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res., 34, W310-W314.
    • (2006) Nucleic Acids Res , vol.34
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 33
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen,R., Li,L. and Weng,Z. (2003) ZDOCK: An initial-stage protein-docking algorithm. Proteins, 52, 80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 35
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez,C., Boelens,R. and Bonvin,A.M. (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc., 125, 1731-1737.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 37
    • 42649122289 scopus 로고    scopus 로고
    • 3D-Garden: A system for modelling protein-protein complexes based on conformational re.nement of ensembles generated with the marching cubes algorithm
    • Lesk,V.I. and Sternberg,M.J. (2008) 3D-Garden: A system for modelling protein-protein complexes based on conformational re.nement of ensembles generated with the marching cubes algorithm. Bioinformatics, 24 1137-1144.
    • (2008) Bioinformatics , vol.24 , pp. 1137-1144
    • Lesk, V.I.1    Sternberg, M.J.2
  • 38
    • 21644446566 scopus 로고    scopus 로고
    • Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues
    • Terashi,G., Takeda-Shitaka,M., Takaya,D., Komatsu,K. and Umeyama,H. (2005) Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues. Proteins, 60, 289-295.
    • (2005) Proteins , vol.60 , pp. 289-295
    • Terashi, G.1    Takeda-Shitaka, M.2    Takaya, D.3    Komatsu, K.4    Umeyama, H.5
  • 39
    • 48449105393 scopus 로고    scopus 로고
    • The RosettaDock server for local protein-protein docking
    • Lyskov,S. and Gray,J.J. (2008) The RosettaDock server for local protein-protein docking. Nucleic Acids Res., 36, W233-W238.
    • (2008) Nucleic Acids Res , vol.36
    • Lyskov, S.1    Gray, J.J.2
  • 40
    • 9944237833 scopus 로고    scopus 로고
    • Complementarity of structure ensembles in protein-protein binding
    • Grunberg,R., Leckner,J. and Nilges,M. (2004) Complementarity of structure ensembles in protein-protein binding. Structure, 12 2125-2136.
    • (2004) Structure , vol.12 , pp. 2125-2136
    • Grunberg, R.1    Leckner, J.2    Nilges, M.3
  • 41
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking
    • Smith,G.R., Sternberg,M.J. and Bates,P.A. (2005) The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with an application to protein-protein docking. J. Mol. Biol., 347, 1077-1101.
    • (2005) J. Mol. Biol , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 42
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard,K., Prevost,C. and Zacharias,M. (2006) Accounting for loop flexibility during protein-protein docking. Proteins, 62, 956-969.
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 43
    • 36749057349 scopus 로고    scopus 로고
    • Implicit flexibility in protein docking: Cross-docking and local refinement
    • Krol,M., Chaleil,R.A., Tournier,A.L. and Bates,P.A. (2007) Implicit flexibility in protein docking: Cross-docking and local refinement. Proteins, 69, 750-757.
    • (2007) Proteins , vol.69 , pp. 750-757
    • Krol, M.1    Chaleil, R.A.2    Tournier, A.L.3    Bates, P.A.4
  • 46
    • 33748988479 scopus 로고    scopus 로고
    • Long loop prediction using the protein local optimization program
    • Zhu,K., Pincus,D.L., Zhao,S. and Friesner,R.A. (2006) Long loop prediction using the protein local optimization program. Proteins, 65, 438-452.
    • (2006) Proteins , vol.65 , pp. 438-452
    • Zhu, K.1    Pincus, D.L.2    Zhao, S.3    Friesner, R.A.4
  • 47
    • 0346103679 scopus 로고    scopus 로고
    • Rapid protein fold determination using unassigned NMR data
    • Meiler,J. and Baker,D. (2003) Rapid protein fold determination using unassigned NMR data. Proc. Natl Acad. Sci. USA, 100, 15404-15409.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 15404-15409
    • Meiler, J.1    Baker, D.2
  • 50
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures
    • Kraulis,P.J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures. J. Appl. Cryst., 24, 946-950.
    • (1991) J. Appl. Cryst , vol.24 , pp. 946-950
    • Kraulis, P.J.1


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