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Volumn 78, Issue 6, 2010, Pages 1503-1519

FiberDock: Flexible induced-fit backbone refinement in molecular docking

Author keywords

Backbone flexibility; Flexible docking; Modeling protein protein docking; Normal modes; Prediction of protein protein interactions

Indexed keywords

ACCURACY; ARTICLE; CALCULATION; MOLECULAR DOCKING; MOLECULAR INTERACTION; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION;

EID: 77951232176     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22668     Document Type: Article
Times cited : (165)

References (53)
  • 2
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R. Folding and binding cascades: dynamic landscapes and population shifts. Protein Sci 2000; 9: 10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 4
    • 0037470496 scopus 로고    scopus 로고
    • Antibody multispecificity mediated by conformational diversity
    • James LC, Roversi P, Tawfik DS. Antibody multispecificity mediated by conformational diversity. Science 2003; 299: 1362-1367.
    • (2003) Science , vol.299 , pp. 1362-1367
    • James, L.C.1    Roversi, P.2    Tawfik, D.S.3
  • 5
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma B, Shatsky M, Wolfson HJ, Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci 2002; 11: 184-197.
    • (2002) Protein Sci , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 6
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958; 44: 98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 7
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh CS, Milburn D, Gerstein M, Conformational changes associated with protein-protein interactions. Curr Opin Chem Biol 2004; 14: 1-6.
    • (2004) Curr Opin Chem Biol , vol.14 , pp. 1-6
    • Goh, C.S.1    Milburn, D.2    Gerstein, M.3
  • 8
    • 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. Struct 2004; 12: 2125-2136.
    • (2004) Struct , vol.12 , pp. 2125-2136
    • Grunberg, R.1    Leckner, J.2    Nilges, M.3
  • 9
    • 70350340728 scopus 로고    scopus 로고
    • The role of dynamic conformational ensembles in biomolecular recognition
    • Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009; 5: 789-796.
    • (2009) Nat Chem Biol , vol.5 , pp. 789-796
    • Boehr, D.D.1    Nussinov, R.2    Wright, P.E.3
  • 11
    • 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 GR, Sternberg MJE, Bates PA. 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 2005; 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
  • 12
    • 21644460933 scopus 로고    scopus 로고
    • Docking essential dynamics eigenstructures
    • Mustard D, Ritchie DH. Docking essential dynamics eigenstructures. Proteins 2005; 60: 269-274.
    • (2005) Proteins , vol.60 , pp. 269-274
    • Mustard, D.1    Ritchie, D.H.2
  • 13
    • 36749057349 scopus 로고    scopus 로고
    • Implicit flexibility in protein docking: Cross-docking and local refinement
    • Król M, Chaleil RA, Tournier AL, Bates PA. Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 2007; 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
  • 14
    • 48449094112 scopus 로고    scopus 로고
    • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
    • Chaudhury S, Gray JJ. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles. J Mol Biol 2008; 381: 1068-1087.
    • (2008) J Mol Biol , vol.381 , pp. 1068-1087
    • Chaudhury, S.1    Gray, J.J.2
  • 16
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006; 62: 956-969.
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 17
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin A. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Amer Chem. Soc 2003; 125: 1731-1737.
    • (2003) J Amer Chem. Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.3
  • 18
    • 0038697837 scopus 로고    scopus 로고
    • Guided docking: First step to locate potential binding sites
    • Fitzjohn PW, Bates PA. Guided docking: first step to locate potential binding sites. Proteins 2003; 52: 28-32.
    • (2003) Proteins , vol.52 , pp. 28-32
    • Fitzjohn, P.W.1    Bates, P.A.2
  • 19
    • 21644477228 scopus 로고    scopus 로고
    • Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI
    • Smith GR, Fitzjohn PW, Page CS, Bates PA. Incorporation of flexibility into rigid-body docking: applications in rounds 3-5 of CAPRI. Proteins 2005; 60: 263-268.
    • (2005) Proteins , vol.60 , pp. 263-268
    • Smith, G.R.1    Fitzjohn, P.W.2    Page, C.S.3    Bates, P.A.4
  • 20
    • 34249884544 scopus 로고    scopus 로고
    • Flexible relaxation of rigid-body docking solutions
    • Krol M, Tournier AL, Bates PA. Flexible relaxation of rigid-body docking solutions. Proteins 2007; 68: 159-169.
    • (2007) Proteins , vol.68 , pp. 159-169
    • Krol, M.1    Tournier, A.L.2    Bates, P.A.3
  • 22
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • Wang C, Bradley P, Baker D. Protein-protein docking with backbone flexibility. J Mol Biol 2007; 373: 505-515.
    • (2007) J Mol Biol , vol.373 , pp. 505-515
    • Wang, C.1    Bradley, P.2    Baker, D.3
  • 23
    • 36749075510 scopus 로고    scopus 로고
    • Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12
    • Chaudhury S, Sircar A, Sivasubramanian A, Berrando M, Gray JJ. Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12. Proteins 2007; 69: 793-800.
    • (2007) Proteins , vol.69 , pp. 793-800
    • Chaudhury, S.1    Sircar, A.2    Sivasubramanian, A.3    Berrando, M.4    Gray, J.J.5
  • 24
    • 23344454719 scopus 로고    scopus 로고
    • Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
    • Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization. Nucleic Acids Res 2005; 33: 4496-4506.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4496-4506
    • Lindahl, E.1    Delarue, M.2
  • 25
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    • May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008; 70: 794-809.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 26
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion MM. Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys Rev Lett 1996; 77: 1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 27
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998; 33: 417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 28
    • 1642365068 scopus 로고    scopus 로고
    • New advances in normal mode analysis of supermolecular complexes and applications to structural refinement
    • Ma J. New advances in normal mode analysis of supermolecular complexes and applications to structural refinement. Curr Protein Pept Sci 2004; 5: 119-123.
    • (2004) Curr Protein Pept Sci , vol.5 , pp. 119-123
    • Ma, J.1
  • 29
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001; 14: 1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 30
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for global protein deformability during protein-protein and protein-ligand docking
    • May A, Zacharias M. Accounting for global protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005; 1754: 225-231.
    • (2005) Biochim Biophys Acta , vol.1754 , pp. 225-231
    • May, A.1    Zacharias, M.2
  • 31
    • 33646145523 scopus 로고    scopus 로고
    • Can conformational change be described by only a few normal modes?
    • Petrone P, Pande VS. Can conformational change be described by only a few normal modes? Biophys J 2006; 90: 1583-1593.
    • (2006) Biophys J , vol.90 , pp. 1583-1593
    • Petrone, P.1    Pande, V.S.2
  • 32
    • 48749126860 scopus 로고    scopus 로고
    • Insights into protein flexibility: The relationship between normal modes and conformational change upon protein-protein docking
    • Dobbins SE, Lesk VI, Sternberg MJ. Insights into protein flexibility: the relationship between normal modes and conformational change upon protein-protein docking. Proc Natl Acad Sci USA 2008; 105: 10390-10395.
    • (2008) Proc Natl Acad Sci USA , vol.105 , pp. 10390-10395
    • Dobbins, S.E.1    Lesk, V.I.2    Sternberg, M.J.3
  • 33
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • Cavasotto CN, Kovacs JA, Abagyan RA. Representing receptor flexibility in ligand docking through relevant normal modes. J Am Chem Soc 2005; 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
  • 34
    • 34548317146 scopus 로고    scopus 로고
    • FireDock: Fast interaction refinement in molecular docking
    • Andrusier N, Nussinov R, Wolfson HJ. FireDock: fast interaction refinement in molecular docking. Proteins 2007; 69: 139-159.
    • (2007) Proteins , vol.69 , pp. 139-159
    • Andrusier, N.1    Nussinov, R.2    Wolfson, H.J.3
  • 35
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Schueler-Furman. O, Kuhlman B, Rohi 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    Schueler-Furman, O.3    Kuhlman, B.4    Rohi, C.A.5    Baker, D.6
  • 36
    • 68549106477 scopus 로고    scopus 로고
    • Side chain-positioning as an integer programming problem
    • Eriksson O. Side chain-positioning as an integer programming problem. Lect Notes in Comput Sci 2001; 2149: 128-141.
    • (2001) Lect Notes in Comput Sci , vol.2149 , pp. 128-141
    • Eriksson, O.1
  • 37
    • 77958398767 scopus 로고
    • The convergence of a class of double-rank minimization algorithms
    • Broyden CG. The convergence of a class of double-rank minimization algorithms. J Inst Math Appl 1970; 6: 76-90.
    • (1970) J Inst Math Appl , vol.6 , pp. 76-90
    • Broyden, C.G.1
  • 38
    • 0014825610 scopus 로고
    • A new approach to variable metric algorithms
    • Fletcher R. A new approach to variable metric algorithms. Comput J 1970; 13: 317-322.
    • (1970) Comput J , vol.13 , pp. 317-322
    • Fletcher, R.1
  • 41
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • Dunbrack RL Jr, Canutescu AA. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003; 12: 963-972.
    • (2003) Protein Sci , vol.12 , pp. 963-972
    • Jr, D.R.L.1    Canutescu, A.A.2
  • 42
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez. 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
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 45
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd edition
    • Lensink MF, Wodak SJ, Mendez R. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007; 69: 704-718.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Wodak, S.J.2    Mendez, R.3
  • 46
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005; 60: 150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 49
    • 34447286908 scopus 로고    scopus 로고
    • The third CAPRI assessment meeting, Toronto, Canada, April 20-2.1
    • Janin J, Wodak S. The third CAPRI assessment meeting, Toronto, Canada, April 20-2.1, 2007. Structure 2007; 15: 755-759.
    • (2007) Structure , vol.2007 , Issue.15 , pp. 755-759
    • Janin, J.1    Wodak, S.2
  • 50
    • 21644459373 scopus 로고    scopus 로고
    • Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
    • Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005; 60: 187-194.
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, O.1    Wang, C.2    Baker, D.3
  • 53
    • 36749077465 scopus 로고    scopus 로고
    • Automatic prediction of protein interactions with large scale motion
    • Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins 2007; 69: 764-773.
    • (2007) Proteins , vol.69 , pp. 764-773
    • Schneidman-Duhovny, D.1    Nussinov, R.2    Wolfson, H.J.3


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