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Volumn 60, Issue 2, 2005, Pages 195-201

Docking to single-domain and multiple-domain proteins: Old and new challenges

Author keywords

CAPRI experiment; Evolutionary conserved patches; Hinge movement; Multibody docking; Multistage docking; Protein flexibility; Unbound docking; Weighted docking

Indexed keywords

ACCURACY; COMPLEX FORMATION; CONFERENCE PAPER; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; EXPERIMENT; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR MODEL; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; RIGIDITY; X RAY ANALYSIS;

EID: 21644483402     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20557     Document Type: Conference Paper
Times cited : (29)

References (54)
  • 1
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 2
    • 2942589060 scopus 로고    scopus 로고
    • On proteins, grids, correlations, and docking
    • Eisenstein M, Katchalski-Katzir E. On proteins, grids, correlations, and docking. C R Biol 2004;327:409-420.
    • (2004) C R Biol , vol.327 , pp. 409-420
    • Eisenstein, M.1    Katchalski-Katzir, E.2
  • 3
    • 2942552020 scopus 로고    scopus 로고
    • Protein structure prediction via combinatorial assembly of sub-structural units
    • Inbar Y, Benyamini H, Nussinov R, Wolfson HJ. Protein structure prediction via combinatorial assembly of sub-structural units. Bioinformatics 2003;19(Suppl 1):i158-i168.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Inbar, Y.1    Benyamini, H.2    Nussinov, R.3    Wolfson, H.J.4
  • 4
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 5
    • 0038359596 scopus 로고    scopus 로고
    • Successful discrimination of protein interactions
    • Camacho CJ, Gatchell DW. Successful discrimination of protein interactions. Proteins 2003;52:92-97.
    • (2003) Proteins , vol.52 , pp. 92-97
    • Camacho, C.J.1    Gatchell, D.W.2
  • 6
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • Fernandez-Recio J, Totrov M, Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci 2002;11:280-291.
    • (2002) Protein Sci , vol.11 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 7
    • 9944237833 scopus 로고    scopus 로고
    • Complementarity of structure ensembles in protein-protein binding
    • Grunberg R, Leckner J, Nilges M. Complementarity of structure ensembles in protein-protein binding. Structure 2004;12:2125-2136.
    • (2004) Structure , vol.12 , pp. 2125-2136
    • Grunberg, R.1    Leckner, J.2    Nilges, M.3
  • 8
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12: 1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 9
    • 0003187567 scopus 로고    scopus 로고
    • The atomic structure of protein-protein recognition sites
    • Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999;285:2177-2198.
    • (1999) J Mol Biol , vol.285 , pp. 2177-2198
    • Lo Conte, L.1    Chothia, C.2    Janin, J.3
  • 10
    • 0032897494 scopus 로고    scopus 로고
    • An analysis of conformational changes on protein-protein association: Implications for predictive docking
    • Betts MJ, Sternberg MJ. An analysis of conformational changes on protein-protein association: implications for predictive docking. Protein Eng 1999;12:271-283.
    • (1999) Protein Eng , vol.12 , pp. 271-283
    • Betts, M.J.1    Sternberg, M.J.2
  • 12
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Méndez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Méndez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 13
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992;89:2195-2199.
    • (1992) Proc Natl Acad Sci USA , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1    Shariv, I.2    Eisenstein, M.3    Friesem, A.A.4    Aflalo, C.5    Vakser, I.A.6
  • 15
    • 2642518000 scopus 로고    scopus 로고
    • Hydrophobic complementarity in protein-protein docking
    • Berchanski A, Shapira B, Eisenstein M. Hydrophobic complementarity in protein-protein docking. Proteins 2004;56:130-142.
    • (2004) Proteins , vol.56 , pp. 130-142
    • Berchanski, A.1    Shapira, B.2    Eisenstein, M.3
  • 16
    • 0038187616 scopus 로고    scopus 로고
    • Weighted geometric docking: Incorporating external information in the rotation-translation scan
    • Ben-Zeev E, Eisenstein M. Weighted geometric docking: incorporating external information in the rotation-translation scan. Proteins 2003;52:24-27.
    • (2003) Proteins , vol.52 , pp. 24-27
    • Ben-Zeev, E.1    Eisenstein, M.2
  • 17
    • 0031566966 scopus 로고    scopus 로고
    • Modeling supra-molecular helices: Extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus
    • Eisenstein M, Shariv I, Koren G, Friesem AA, Katchalski-Katzir E. Modeling supra-molecular helices: extension of the molecular surface recognition algorithm and application to the protein coat of the tobacco mosaic virus. J Mol Biol 1997;266:135-143.
    • (1997) J Mol Biol , vol.266 , pp. 135-143
    • Eisenstein, M.1    Shariv, I.2    Koren, G.3    Friesem, A.A.4    Katchalski-Katzir, E.5
  • 18
    • 0038185195 scopus 로고    scopus 로고
    • Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking
    • Heifetz A, Eisenstein M. Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Eng 2003;16:179-185.
    • (2003) Protein Eng , vol.16 , pp. 179-185
    • Heifetz, A.1    Eisenstein, M.2
  • 19
    • 0032568649 scopus 로고    scopus 로고
    • A unified statistical framework for sequence comparison and structure comparison
    • Levitt M, Gerstein M. A unified statistical framework for sequence comparison and structure comparison. Proc Natl Acad Sci USA 1998;95:5913-5920.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 5913-5920
    • Levitt, M.1    Gerstein, M.2
  • 20
    • 0041858013 scopus 로고    scopus 로고
    • Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface
    • Takagi J, Yang Y, Liu JH, Wang JH, Springer TA. Complex between nidogen and laminin fragments reveals a paradigmatic beta-propeller interface. Nature 2003;424:969-974.
    • (2003) Nature , vol.424 , pp. 969-974
    • Takagi, J.1    Yang, Y.2    Liu, J.H.3    Wang, J.H.4    Springer, T.A.5
  • 21
    • 0029967684 scopus 로고    scopus 로고
    • Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site
    • Stetefeld J, Mayer U, Timpl R, Huber R. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site. J Mol Biol 1996;257:644-657.
    • (1996) J Mol Biol , vol.257 , pp. 644-657
    • Stetefeld, J.1    Mayer, U.2    Timpl, R.3    Huber, R.4
  • 22
    • 0029790892 scopus 로고    scopus 로고
    • Site-directed mutagenesis and structural interpretation of the nidogen binding site of the laminin gamma1 chain
    • Poschl E, Mayer U, Stetefeld J, Baumgartner R, Holak TA, Huber R, Timpl R. Site-directed mutagenesis and structural interpretation of the nidogen binding site of the laminin gamma1 chain. EMBO J 1996;15:5154-5159.
    • (1996) EMBO J , vol.15 , pp. 5154-5159
    • Poschl, E.1    Mayer, U.2    Stetefeld, J.3    Baumgartner, R.4    Holak, T.A.5    Huber, R.6    Timpl, R.7
  • 23
    • 17644378441 scopus 로고    scopus 로고
    • Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes
    • Graille M, Zhou C-Z, Receveur-Bréchot V, Collinet B, Declerck N, van Tilbeurgh H. Activation of the LicT transcriptional antiterminator involves a domain swing/lock mechanism provoking massive structural changes. J Biol Chem 2005;280:14780-14789.
    • (2005) J Biol Chem , vol.280 , pp. 14780-14789
    • Graille, M.1    Zhou, C.-Z.2    Receveur-Bréchot, V.3    Collinet, B.4    Declerck, N.5    Van Tilbeurgh, H.6
  • 24
    • 0035898533 scopus 로고    scopus 로고
    • Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator
    • van Tilbeurgh H, Le Coq D, Declerck N. Crystal structure of an activated form of the PTS regulation domain from the LicT transcriptional antiterminator. EMBO J 2001;20:3789-3799.
    • (2001) EMBO J , vol.20 , pp. 3789-3799
    • Van Tilbeurgh, H.1    Le Coq, D.2    Declerck, N.3
  • 26
    • 0029014434 scopus 로고
    • The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution
    • Rey FA, Heinz FX, Mandl C, Kunz C, Harrison SC. The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution. Nature 1995;375:291-298.
    • (1995) Nature , vol.375 , pp. 291-298
    • Rey, F.A.1    Heinz, F.X.2    Mandl, C.3    Kunz, C.4    Harrison, S.C.5
  • 29
    • 0031569395 scopus 로고    scopus 로고
    • A cohesin domain from Clostridium thermocellum: The crystal structure provides new insights into cellulosome assembly
    • Shimon LJ, Bayer EA, Morag E, Lamed R, Yaron S, Shoham Y, Frolow F. A cohesin domain from Clostridium thermocellum: the crystal structure provides new insights into cellulosome assembly. Structure 1997;5:381-390.
    • (1997) Structure , vol.5 , pp. 381-390
    • Shimon, L.J.1    Bayer, E.A.2    Morag, E.3    Lamed, R.4    Yaron, S.5    Shoham, Y.6    Frolow, F.7
  • 30
    • 0035970297 scopus 로고    scopus 로고
    • Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain
    • Lytle BL, Volkman BF, Westler WM, Heckman MP, Wu JH. Solution structure of a type I dockerin domain, a novel prokaryotic, extracellular calcium-binding domain. J Mol Biol 2001;307: 745-753.
    • (2001) J Mol Biol , vol.307 , pp. 745-753
    • Lytle, B.L.1    Volkman, B.F.2    Westler, W.M.3    Heckman, M.P.4    Wu, J.H.5
  • 31
    • 0033613077 scopus 로고    scopus 로고
    • Cellulosome from Clostridium cellulolyticum: Molecular study of the dockerin/cohesin interaction
    • Fierobe HP, Pages S, Belaich A, Champ S, Lexa D, Belaich JP. Cellulosome from Clostridium cellulolyticum: molecular study of the dockerin/cohesin interaction. Biochemistry 1999;38:12822-12832.
    • (1999) Biochemistry , vol.38 , pp. 12822-12832
    • Fierobe, H.P.1    Pages, S.2    Belaich, A.3    Champ, S.4    Lexa, D.5    Belaich, J.P.6
  • 32
    • 0035971154 scopus 로고    scopus 로고
    • Cohesin-dockerin interaction in cellulosome assembly: A single hydroxyl group of a dockerin domain distinguishes between nonrecognition and high affinity recognition
    • Mechaly A, Fierobe HP, Belaich A, Belaich JP, Lamed R, Shoham Y, Bayer EA. Cohesin-dockerin interaction in cellulosome assembly: a single hydroxyl group of a dockerin domain distinguishes between nonrecognition and high affinity recognition. J Biol Chem 2001;276:9883-9888.
    • (2001) J Biol Chem , vol.276 , pp. 9883-9888
    • Mechaly, A.1    Fierobe, H.P.2    Belaich, A.3    Belaich, J.P.4    Lamed, R.5    Shoham, Y.6    Bayer, E.A.7
  • 33
    • 0036315557 scopus 로고    scopus 로고
    • Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily
    • He XL, Grigg ME, Boothroyd JC, Garcia KC. Structure of the immunodominant surface antigen from the Toxoplasma gondii SRS superfamily. Nat Struct Biol 2002;9:606-611.
    • (2002) Nat Struct Biol , vol.9 , pp. 606-611
    • He, X.L.1    Grigg, M.E.2    Boothroyd, J.C.3    Garcia, K.C.4
  • 34
  • 35
    • 0029094754 scopus 로고
    • Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1
    • Goldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J. Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 1995;376:745-753.
    • (1995) Nature , vol.376 , pp. 745-753
    • Goldberg, J.1    Huang, H.B.2    Kwon, Y.G.3    Greengard, P.4    Nairn, A.C.5    Kuriyan, J.6
  • 36
    • 0030977268 scopus 로고    scopus 로고
    • Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1
    • Egloff MP, Johnson DF, Moorhead G, Cohen PT, Cohen P, Barford D. Structural basis for the recognition of regulatory subunits by the catalytic subunit of protein phosphatase 1. EMBO J 1997;16: 1876-1887.
    • (1997) EMBO J , vol.16 , pp. 1876-1887
    • Egloff, M.P.1    Johnson, D.F.2    Moorhead, G.3    Cohen, P.T.4    Cohen, P.5    Barford, D.6
  • 37
    • 2342447390 scopus 로고    scopus 로고
    • Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein
    • Graille M, Mora L, Buckingham RH, Van Tilbeurgh H, De Zamaroczy M. Structural inhibition of the colicin D tRNase by the tRNA-mimicking immunity protein. EMBO J 2004;23:1474-1482.
    • (2004) EMBO J , vol.23 , pp. 1474-1482
    • Graille, M.1    Mora, L.2    Buckingham, R.H.3    Van Tilbeurgh, H.4    De Zamaroczy, M.5
  • 38
    • 0036589208 scopus 로고    scopus 로고
    • Importation of nuclease colicins into E. coli cells: Endoproteolytic cleavage and its prevention by the immunity protein
    • de Zamaroczy M, Buckingham RH. Importation of nuclease colicins into E. coli cells: endoproteolytic cleavage and its prevention by the immunity protein. Biochimie 2002;84:423-432.
    • (2002) Biochimie , vol.84 , pp. 423-432
    • De Zamaroczy, M.1    Buckingham, R.H.2
  • 40
    • 0038677006 scopus 로고    scopus 로고
    • Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson)
    • Payan F, Flatman R, Porciero S, Williamson G, Juge N, Roussel A. Structural analysis of xylanase inhibitor protein I (XIP-I), a proteinaceous xylanase inhibitor from wheat (Triticum aestivum, var. Soisson). Biochem J 2003;372:399-405.
    • (2003) Biochem J , vol.372 , pp. 399-405
    • Payan, F.1    Flatman, R.2    Porciero, S.3    Williamson, G.4    Juge, N.5    Roussel, A.6
  • 42
    • 0037113937 scopus 로고    scopus 로고
    • Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger
    • Tahir TA, Benin JG, Flatman R, Roussel A, Roepstorff P, Williamson G, Juge N. Specific characterization of substrate and inhibitor binding sites of a glycosyl hydrolase family 11 xylanase from Aspergillus niger. J Biol Chem 2002;277:44035-44043.
    • (2002) J Biol Chem , vol.277 , pp. 44035-44043
    • Tahir, T.A.1    Benin, J.G.2    Flatman, R.3    Roussel, A.4    Roepstorff, P.5    Williamson, G.6    Juge, N.7
  • 43
    • 4143057133 scopus 로고    scopus 로고
    • Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I
    • Sansen S, De Ranter CJ, Gebruers K, Brijs K, Courtin CM, Delcour JA, Rabijns A. Structural basis for inhibition of Aspergillus niger xylanase by Triticum aestivum xylanase inhibitor-I. J Biol Chem 2004;279:36022-36028.
    • (2004) J Biol Chem , vol.279 , pp. 36022-36028
    • Sansen, S.1    De Ranter, C.J.2    Gebruers, K.3    Brijs, K.4    Courtin, C.M.5    Delcour, J.A.6    Rabijns, A.7
  • 44
    • 0030592470 scopus 로고    scopus 로고
    • Three-dimensional structure of endo-1,4-beta-xylanase I from Aspergillus niger: Molecular basis for its low pH optimum
    • Krengel U, Dijkstra BW. Three-dimensional structure of endo-1,4-beta-xylanase I from Aspergillus niger: molecular basis for its low pH optimum. J Mol Biol 1996;263:70-78.
    • (1996) J Mol Biol , vol.263 , pp. 70-78
    • Krengel, U.1    Dijkstra, B.W.2
  • 51
    • 0344406096 scopus 로고    scopus 로고
    • Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa: Comparison of twelve xylanases in relation to their thermal stability
    • Hakulinen N, Turunen O, Janis J, Leisola M, Rouvinen J. Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa: comparison of twelve xylanases in relation to their thermal stability. Eur J Biochem 2003;270:1399-1412.
    • (2003) Eur J Biochem , vol.270 , pp. 1399-1412
    • Hakulinen, N.1    Turunen, O.2    Janis, J.3    Leisola, M.4    Rouvinen, J.5
  • 53
    • 0032829397 scopus 로고    scopus 로고
    • Predictive estimation of protein linear epitopes by using the program PEOPLE
    • Alix AJP. Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine 2000;18:311-314.
    • (2000) Vaccine , vol.18 , pp. 311-314
    • Alix, A.J.P.1
  • 54
    • 0035695915 scopus 로고    scopus 로고
    • Structural insights into the regulation of bacterial signalling proteins containing PRDs
    • van Tilbeurgh H, Declerck N. Structural insights into the regulation of bacterial signalling proteins containing PRDs. Curr Opin Struct Biol 2001;11:685-693.
    • (2001) Curr Opin Struct Biol , vol.11 , pp. 685-693
    • Van Tilbeurgh, H.1    Declerck, N.2


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