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Volumn 38, Issue SUPPL. 2, 2010, Pages

FiberDock: A web server for flexible induced-fit backbone refinement in molecular docking

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ALGORITHM; ARTICLE; BIOINFORMATICS; CLIENT SERVER APPLICATION; CONFORMATIONAL TRANSITION; MOLECULAR DOCKING; PREDICTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER INTERFACE; COMPUTER PROGRAM; INTERNET; PROTEIN ANALYSIS; PROTEIN CONFORMATION;

EID: 77954267296     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq373     Document Type: Article
Times cited : (80)

References (33)
  • 2
    • 23344454719 scopus 로고    scopus 로고
    • Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
    • Lindahl,E. and Delarue,M. (2005) Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res., 33, 4496-4506.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4496-4506
    • Lindahl, E.1    Delarue, M.2
  • 3
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global exibility during systematic protein-protein docking
    • May,A. and Zacharias,M. (2008) Energy minimization in low-frequency normal modes to efficiently allow for global exibility during systematic protein-protein docking. Proteins, 70, 794-809.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 4
    • 36749035257 scopus 로고    scopus 로고
    • Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
    • May,A. and Zacharias,M. (2007) Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility. Proteins, 69, 774-780.
    • (2007) Proteins , vol.69 , pp. 774-780
    • May, A.1    Zacharias, M.2
  • 5
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang,C., Bradley,P. and Baker,D. (2007) Protein-protein docking with backbone flexibility. J. Mol. Biol., 373, 503-519.
    • (2007) J. Mol. Biol. , vol.373 , pp. 503-519
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 6
    • 36749075510 scopus 로고    scopus 로고
    • Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
    • Chaudhury,S., Sircar,A., Sivasubramanian,A., Berrondo,M. and Gray,J.J. (2007) Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins, 69, 793-800.
    • (2007) Proteins , vol.69 , pp. 793-800
    • Chaudhury, S.1    Sircar, A.2    Sivasubramanian, A.3    Berrondo, M.4    Gray, J.J.5
  • 7
    • 0038697837 scopus 로고    scopus 로고
    • Guided docking: first step to locate potential binding sites
    • Fitzjohn,P.W. and Bates,P.A. (2003) Guided docking: first step to locate potential binding sites. Proteins, 52, 28-32.
    • (2003) Proteins , vol.52 , pp. 28-32
    • Fitzjohn, P.W.1    Bates, P.A.2
  • 8
    • 36749057349 scopus 로고    scopus 로고
    • Implicit flexibility in protein docking: cross-docking and local refinement
    • Król,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
    • Król, M.1    Chaleil, R.A.2    Tournier, A.L.3    Bates, P.A.4
  • 10
    • 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
  • 11
    • 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, 310-314.
    • (2006) Nucleic Acids Res , vol.34 , pp. 310-314
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 12
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • Ritchie,D.W. and Kemp,G.J.L. (2000) Protein docking using spherical polar Fourier correlations. Proteins, 39, 178-194.
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.L.2
  • 14
    • 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
  • 15
    • 33747858757 scopus 로고    scopus 로고
    • NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
    • Lindahl,E., Azuara,C., Koehl,P. and Delarue,M. (2006) NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Res., 34, W52-W56.
    • (2006) Nucleic Acids Res , vol.34
    • Lindahl, E.1    Azuara, C.2    Koehl, P.3    Delarue, M.4
  • 17
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • Dominguez,C., Boelens,R. and Bonvin,A. (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.3
  • 18
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen,K. (1998) Analysis of domain motions by approximate normal mode calculations. Proteins, 33, 417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 19
    • 33646145523 scopus 로고    scopus 로고
    • Can conformational change be described by only a few normal modes?
    • Petrone,P. and Pande,V.S. (2006) Can conformational change be described by only a few normal modes? Biophys. J., 90, 1583-1593.
    • (2006) Biophys. J. , vol.90 , pp. 1583-1593
    • Petrone, P.1    Pande, V.S.2
  • 20
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto,C.N., Kovacs,J.A. and Abagyan,R.A. (2005) Representing receptor flexibility in ligand docking through relevant normal modes. J. Am. Chem. Soc., 127, 9632-9640.
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 21
    • 77951232176 scopus 로고    scopus 로고
    • FiberDock: flexible induced-fit backbone refinement in molecular docking
    • Mashiach,E., Nussinov,R. and Wolfson,H.J. (2009) FiberDock: flexible induced-fit backbone refinement in molecular docking. Proteins, 78, 1503-1519.
    • (2009) Proteins , vol.78 , pp. 1503-1519
    • Mashiach, E.1    Nussinov, R.2    Wolfson, H.J.3
  • 22
    • 34548317146 scopus 로고    scopus 로고
    • FireDock: fast interaction refinement in molecular docking
    • Andrusier,N., Nussinov,R. and Wolfson,H.J. (2007) FireDock: fast interaction refinement in molecular docking. Proteins, 69, 139-159.
    • (2007) Proteins , vol.69 , pp. 139-159
    • Andrusier, N.1    Nussinov, R.2    Wolfson, H.J.3
  • 23
    • 68549106477 scopus 로고    scopus 로고
    • Side chain-positioning as an integer programming problem
    • Eriksson,O. (2001) Side chain-positioning as an integer programming problem. Lect. Notes Comput. Sci., 2149, 128-141.
    • (2001) Lect. Notes Comput. Sci. , vol.2149 , pp. 128-141
    • Eriksson, O.1
  • 24
    • 77958398767 scopus 로고
    • The convergence of a class of double-rank minimization algorithms
    • Broyden,C.G. (1970) The convergence of a class of double-rank minimization algorithms. J. Inst. Math. Appl., 6, 76-90.
    • (1970) J. Inst. Math. Appl. , vol.6 , pp. 76-90
    • Broyden, C.G.1
  • 25
    • 0014825610 scopus 로고
    • A new approach to variable metric algorithms
    • Fletcher,R. (1970) A new approach to variable metric algorithms. The Computer Journal, 13, 317-322.
    • (1970) The Computer Journal , vol.13 , pp. 317-322
    • Fletcher, R.1
  • 29
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen,R. and Weng,Z. (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47, 281-294.
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 30
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with application to protein-protein docking
    • Smith,G.R., Sternberg,M.J.E. and Bates,P.A. (2005) The relationship between the flexibility of proteins and their conformational states on forming protein-protein complexes with 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.E.2    Bates, P.A.3
  • 32
    • 7944225979 scopus 로고    scopus 로고
    • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking
    • Li,X., Keskin,O., Ma,B., Nussinov,R. and Liang,J. (2004) Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. J. Mol. Biol., 344, 781-795.
    • (2004) J. Mol. Biol. , vol.344 , pp. 781-795
    • Li, X.1    Keskin, O.2    Ma, B.3    Nussinov, R.4    Liang, J.5
  • 33
    • 33746124556 scopus 로고    scopus 로고
    • Biomolecules in the computer: jmol to the rescue
    • Herraez,A. (2006) Biomolecules in the computer: jmol to the rescue. Biochem. Mol. Biol. Educ., 34, 255-261.
    • (2006) Biochem. Mol. Biol. Educ. , vol.34 , pp. 255-261
    • Herraez, A.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.