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Volumn 60, Issue 2, 2005, Pages 232-238

Data-driven docking: HADDOCK'S adventures in CAPRI

Author keywords

Biomolecular complexes; Flexible docking; HADDOCK; Interface prediction

Indexed keywords

EPITOPE; LIGAND; RECEPTOR;

EID: 21644454184     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20563     Document Type: Conference Paper
Times cited : (75)

References (40)
  • 2
    • 12544256528 scopus 로고    scopus 로고
    • Data-driven docking for the study of biomolecular complexes
    • van Dijk ADJ, Boelens R, Bonvin AMJJ. Data-driven docking for the study of biomolecular complexes. FEBS J 2005;272:293-312.
    • (2005) FEBS J , vol.272 , pp. 293-312
    • Van Dijk, A.D.J.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 3
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AMJJ. HADDOCK: A protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.J.J.3
  • 4
    • 33645941402 scopus 로고
    • The OPLS Potential functions for proteins: Energy minimizations for crystals of cyclin peptides and crambin
    • Jorgensen WL, Tirado-rives J. The OPLS Potential functions for proteins: energy minimizations for crystals of cyclin peptides and crambin. J Am Chem Soc 1988;110:1657-1666.
    • (1988) J Am Chem Soc , vol.110 , pp. 1657-1666
    • Jorgensen, W.L.1    Tirado-rives, J.2
  • 5
    • 0020997912 scopus 로고
    • Dictionary of Protein Secondary Structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W, Sander C. Dictionary of Protein Secondary Structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 6
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou HX, Shan YB. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44:336-343.
    • (2001) Proteins , vol.44 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.B.2
  • 10
    • 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
  • 11
    • 0027383637 scopus 로고
    • A calculation strategy for the structure determination of symmetrical dimers by H-1-NMR
    • Nilges M. A calculation strategy for the structure determination of symmetrical dimers by H-1-NMR. Proteins 1993;17:297-309.
    • (1993) Proteins , vol.17 , pp. 297-309
    • Nilges, M.1
  • 13
    • 0029795282 scopus 로고    scopus 로고
    • Structural requirements for low-pH-induced rearrangements in the envelope glycoprotein of tick-borne encephalitis virus
    • Stiasny K, Allison SL, MarchlerBauer A, Kunz C, Heinz FX. Structural requirements for low-pH-induced rearrangements in the envelope glycoprotein of tick-borne encephalitis virus. J Virol 1996;70:8142-8147.
    • (1996) J Virol , vol.70 , pp. 8142-8147
    • Stiasny, K.1    Allison, S.L.2    Marchlerbauer, A.3    Kunz, C.4    Heinz, F.X.5
  • 14
    • 0035051804 scopus 로고    scopus 로고
    • Mutational evidence for an internal fusion peptide in flavivirus envelope protein e
    • Allison SL, Schalich J, Stiasny K, Mandl CW, Heinz FX. Mutational evidence for an internal fusion peptide in flavivirus envelope protein E. J Virol 2001;75:4268-4275.
    • (2001) J Virol , vol.75 , pp. 4268-4275
    • Allison, S.L.1    Schalich, J.2    Stiasny, K.3    Mandl, C.W.4    Heinz, F.X.5
  • 15
    • 0036198006 scopus 로고    scopus 로고
    • Membrane interactions of the tick-borne encephalitis virus fusion protein e at low pH
    • Stiasny K, Allison SL, Schalich J, Heinz FX. Membrane interactions of the tick-borne encephalitis virus fusion protein E at low pH. J Virol 2002;76:3784-3790.
    • (2002) J Virol , vol.76 , pp. 3784-3790
    • Stiasny, K.1    Allison, S.L.2    Schalich, J.3    Heinz, F.X.4
  • 16
    • 0032989258 scopus 로고    scopus 로고
    • Mapping of functional elements in the stem-anchor region of tick-borne encephalitis virus envelope protein e
    • Allison SL, Stiasny K, Stadler K, Mandl CW, Heinz FX. Mapping of functional elements in the stem-anchor region of tick-borne encephalitis virus envelope protein E. J Virol 1999;73:5605-5612.
    • (1999) J Virol , vol.73 , pp. 5605-5612
    • Allison, S.L.1    Stiasny, K.2    Stadler, K.3    Mandl, C.W.4    Heinz, F.X.5
  • 18
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31:3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 19
    • 0031718310 scopus 로고    scopus 로고
    • Homology modeling, model and software evaluation: Three related resources
    • Rodriguez R, Chinea G, Lopez N, Pons T, Vriend G. Homology modeling, model and software evaluation: three related resources. Bioinformatics 1998;14:523-528.
    • (1998) Bioinformatics , vol.14 , pp. 523-528
    • Rodriguez, R.1    Chinea, G.2    Lopez, N.3    Pons, T.4    Vriend, G.5
  • 20
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: A package for molecular simulation and trajectory analysis
    • Lindahl E, Hess B, van der Spoel D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 2001;7: 306-317.
    • (2001) J Mol Model , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    Van Der Spoel, D.3
  • 21
    • 0037133275 scopus 로고    scopus 로고
    • Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA
    • Miras I, Schaeffer F, Beguin P, Alzari PM. Mapping by site-directed mutagenesis of the region responsible for cohesin-dockerin interaction on the surface of the seventh cohesin domain of Clostridium thermocellum CipA. Biochemistry 2002;41:2115-2119.
    • (2002) Biochemistry , vol.41 , pp. 2115-2119
    • Miras, I.1    Schaeffer, F.2    Beguin, P.3    Alzari, P.M.4
  • 22
    • 0037133136 scopus 로고    scopus 로고
    • Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity
    • Schaeffer F, Matuschek M, Guglielmi G, Miras I, Alzari PM, Beguin P. Duplicated dockerin subdomains of Clostridium thermocellum endoglucanase CelD bind to a cohesin domain of the scaffolding protein CipA with distinct thermodynamic parameters and a negative cooperativity. Biochemistry 2002;41:2106-2114.
    • (2002) Biochemistry , vol.41 , pp. 2106-2114
    • Schaeffer, F.1    Matuschek, M.2    Guglielmi, G.3    Miras, I.4    Alzari, P.M.5    Beguin, P.6
  • 23
    • 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
  • 26
    • 0034822446 scopus 로고    scopus 로고
    • Anti-SAG1 peptide antibodies inhibit the penetration of Toxoplasma gondii tachyzoites into enterocyte cell lines
    • Velge-Roussel F, Dimier-Poisson I, Buzoni-Gatel D, Bout D. Anti-SAG1 peptide antibodies inhibit the penetration of Toxoplasma gondii tachyzoites into enterocyte cell lines. Parasitology 2001;123:225-233.
    • (2001) Parasitology , vol.123 , pp. 225-233
    • Velge-Roussel, F.1    Dimier-Poisson, I.2    Buzoni-Gatel, D.3    Bout, D.4
  • 28
    • 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 PTW, 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.W.4    Cohen, P.5    Barford, D.6
  • 29
    • 0000606386 scopus 로고    scopus 로고
    • Study of the subunit interactions in myosin phosphatase by surface plasmon resonance
    • Toth A, Kiss E, Herberg FW, Gergely P, Hartshorne DJ, Erdodi F. Study of the subunit interactions in myosin phosphatase by surface plasmon resonance. Eur J Biochem 2000;267:1687-1697.
    • (2000) Eur J Biochem , vol.267 , pp. 1687-1697
    • Toth, A.1    Kiss, E.2    Herberg, F.W.3    Gergely, P.4    Hartshorne, D.J.5    Erdodi, F.6
  • 30
    • 0031034680 scopus 로고    scopus 로고
    • Interactions of the subunits of smooth muscle myosin phosphatase
    • Hirano K, Phan BC, Hartshorne DJ. Interactions of the subunits of smooth muscle myosin phosphatase. J Biol Chem 1997;272: 3683-3688.
    • (1997) J Biol Chem , vol.272 , pp. 3683-3688
    • Hirano, K.1    Phan, B.C.2    Hartshorne, D.J.3
  • 32
    • 0034881923 scopus 로고    scopus 로고
    • Cleavage of colicin D is necessary for cell killing and requires the inner membrane peptidase LepB
    • de Zamaroczy M, Mora L, Lecuyer A, Geli V, Buckingham RH. Cleavage of colicin D is necessary for cell killing and requires the inner membrane peptidase LepB. Mol Cell 2001;8:159-168.
    • (2001) Mol Cell , vol.8 , pp. 159-168
    • Zamaroczy, M.1    Mora, L.2    Lecuyer, A.3    Geli, V.4    Buckingham, R.H.5
  • 33
    • 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
  • 40
    • 10844273275 scopus 로고    scopus 로고
    • The impact of protein flexibility on protein-protein docking
    • Ehrlich LP, Nilges M, Wade RC. The impact of protein flexibility on protein-protein docking. Proteins 2005;58:126-133.
    • (2005) Proteins , vol.58 , pp. 126-133
    • Ehrlich, L.P.1    Nilges, M.2    Wade, R.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.