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Volumn 373, Issue 2, 2007, Pages 503-519

Protein-Protein Docking with Backbone Flexibility

Author keywords

conformational change; flexible backbone docking; loop modeling; Monte Carlo minimization; protein protein docking

Indexed keywords

ARTICLE; CONFORMATIONAL TRANSITION; MOLECULAR DOCKING; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE;

EID: 34548861782     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.07.050     Document Type: Article
Times cited : (356)

References (49)
  • 1
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., Knight J.R., et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403 (2000) 623-627
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1    Giot, L.2    Cagney, G.3    Mansfield, T.A.4    Judson, R.S.5    Knight, J.R.6
  • 2
    • 0037050026 scopus 로고    scopus 로고
    • Functional organization of the yeast proteome by systematic analysis of protein complexes
    • Gavin A.C., Bosche M., Krause R., Grandi P., Marzioch M., Bauer A., et al. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415 (2002) 141-147
    • (2002) Nature , vol.415 , pp. 141-147
    • Gavin, A.C.1    Bosche, M.2    Krause, R.3    Grandi, P.4    Marzioch, M.5    Bauer, A.6
  • 4
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: is the glass half-full or half-empty?
    • Vajda S., and Camacho C.J. Protein-protein docking: is the glass half-full or half-empty?. Trends Biotechnol. 22 (2004) 110-116
    • (2004) Trends Biotechnol. , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 6
    • 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., and Wodak S.J. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 52 (2003) 51-67
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 7
    • 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. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 60 (2005) 150-169
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 8
    • 1342302339 scopus 로고    scopus 로고
    • Conformational changes associated with protein-protein interactions
    • Goh C.S., Milburn D., and Gerstein M. Conformational changes associated with protein-protein interactions. Curr. Opin. Struct. Biol. 14 (2004) 104-109
    • (2004) Curr. Opin. Struct. Biol. , vol.14 , pp. 104-109
    • Goh, C.S.1    Milburn, D.2    Gerstein, M.3
  • 9
    • 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. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125 (2003) 1731-1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 10
    • 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. 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 (2005) 1077-1101
    • (2005) J. Mol. Biol. , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.2    Bates, P.A.3
  • 11
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K., Prevost C., and Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 62 (2006) 956-969
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 13
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray J.J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C.A., and Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J. Mol. Biol. 331 (2003) 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
  • 14
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C., Schueler-Furman O., and Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci. 14 (2005) 1328-1339
    • (2005) Protein Sci. , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 15
    • 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., and 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 60 (2005) 187-194
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, O.1    Wang, C.2    Baker, D.3
  • 16
    • 33751118503 scopus 로고    scopus 로고
    • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    • Bradley P., and Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 65 (2006) 922-929
    • (2006) Proteins , vol.65 , pp. 922-929
    • Bradley, P.1    Baker, D.2
  • 17
    • 0020831001 scopus 로고
    • A method of rapid calculation of a 2nd derivative matrix of conformational energy for large molecules
    • Noguti T., and Go N. A method of rapid calculation of a 2nd derivative matrix of conformational energy for large molecules. J. Phys. Soc. Jpn. 52 (1983) 3685-3690
    • (1983) J. Phys. Soc. Jpn. , vol.52 , pp. 3685-3690
    • Noguti, T.1    Go, N.2
  • 18
    • 0021586472 scopus 로고
    • Rapid calculation of 1st and 2nd derivatives of conformational energy with respect to dihedral angles for proteins-general recurrent equations
    • Abe H., Braun W., Noguti T., and Go N. Rapid calculation of 1st and 2nd derivatives of conformational energy with respect to dihedral angles for proteins-general recurrent equations. Comput. Chem. 8 (1984) 239-247
    • (1984) Comput. Chem. , vol.8 , pp. 239-247
    • Abe, H.1    Braun, W.2    Noguti, T.3    Go, N.4
  • 19
    • 0242362161 scopus 로고    scopus 로고
    • Combining local-structure, fold-recognition, and new fold methods for protein structure prediction
    • Karplus K., Karchin R., Draper J., Casper J., Mandel-Gutfreund Y., Diekhans M., and Hughey R. Combining local-structure, fold-recognition, and new fold methods for protein structure prediction. Proteins 53 (2003) 491-496
    • (2003) Proteins , vol.53 , pp. 491-496
    • Karplus, K.1    Karchin, R.2    Draper, J.3    Casper, J.4    Mandel-Gutfreund, Y.5    Diekhans, M.6    Hughey, R.7
  • 20
    • 84986522918 scopus 로고
    • ICM-a new method for protein modeling and design-applications to docking and structure prediction from the distorted native conformation
    • Abagyan R., Totrov M., and Kuznetsov D. ICM-a new method for protein modeling and design-applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15 (1994) 488-506
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 21
    • 0024609784 scopus 로고
    • New methodology for computer-aided modeling of biomolecular structure and dynamics. 1. Non-cyclic structures
    • Mazur A.K., and Abagyan R.A. New methodology for computer-aided modeling of biomolecular structure and dynamics. 1. Non-cyclic structures. J. Biomol. Struct. Dyn. 6 (1989) 815-832
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 815-832
    • Mazur, A.K.1    Abagyan, R.A.2
  • 22
    • 0024609825 scopus 로고
    • New methodology for computer-aided modeling of biomolecular structure and dynamics. 2. Local deformations and cycles
    • Abagyan R.A., and Mazur A.K. New methodology for computer-aided modeling of biomolecular structure and dynamics. 2. Local deformations and cycles. J. Biomol. Struct. Dyn. 6 (1989) 833-845
    • (1989) J. Biomol. Struct. Dyn. , vol.6 , pp. 833-845
    • Abagyan, R.A.1    Mazur, A.K.2
  • 23
    • 0036149480 scopus 로고    scopus 로고
    • Soft protein-protein docking in internal coordinates
    • Fernandez-Recio J., Totrov M., and Abagyan R. Soft protein-protein docking in internal coordinates. Protein Sci. 11 (2002) 280-291
    • (2002) Protein Sci. , vol.11 , pp. 280-291
    • Fernandez-Recio, J.1    Totrov, M.2    Abagyan, R.3
  • 24
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • Cavasotto C.N., and Abagyan R.A. Protein flexibility in ligand docking and virtual screening to protein kinases. J. Mol. Biol. 337 (2004) 209-225
    • (2004) J. Mol. Biol. , vol.337 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 27
    • 0028070557 scopus 로고
    • Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement
    • Rice L.M., and Brunger A.T. Torsion angle dynamics: reduced variable conformational sampling enhances crystallographic structure refinement. Proteins 19 (1994) 277-290
    • (1994) Proteins , vol.19 , pp. 277-290
    • Rice, L.M.1    Brunger, A.T.2
  • 28
    • 0035742323 scopus 로고    scopus 로고
    • Internal coordinates for molecular dynamics and minimization in structure determination and refinement
    • Schwieters C.D., and Clore G.M. Internal coordinates for molecular dynamics and minimization in structure determination and refinement. J. Magn. Reson. 152 (2001) 288-302
    • (2001) J. Magn. Reson. , vol.152 , pp. 288-302
    • Schwieters, C.D.1    Clore, G.M.2
  • 29
    • 33846471085 scopus 로고    scopus 로고
    • Prediction of structures of multidomain proteins from structures of the individual domains
    • Wollacott A.M., Zanghellini A., Murphy P., and Baker D. Prediction of structures of multidomain proteins from structures of the individual domains. Protein Sci. 16 (2007) 165-175
    • (2007) Protein Sci. , vol.16 , pp. 165-175
    • Wollacott, A.M.1    Zanghellini, A.2    Murphy, P.3    Baker, D.4
  • 30
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z., and Scheraga H.A. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc. Natl Acad. Sci. USA 84 (1987) 6611-6615
    • (1987) Proc. Natl Acad. Sci. USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 32
    • 0034641749 scopus 로고    scopus 로고
    • Native protein sequences are close to optimal for their structures
    • Kuhlman B., and Baker D. Native protein sequences are close to optimal for their structures. Proc. Natl Acad. Sci. USA 97 (2000) 10383-10388
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 10383-10388
    • Kuhlman, B.1    Baker, D.2
  • 33
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with Rosetta
    • Rohl C.A., Strauss C.E., Chivian D., and Baker D. Modeling structurally variable regions in homologous proteins with Rosetta. Proteins 55 (2004) 656-677
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 34
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: a robotics algorithm for protein loop closure
    • Canutescu A.A., and Dunbrack Jr. R.L. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci. 12 (2003) 963-972
    • (2003) Protein Sci. , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 35
  • 36
    • 36749066580 scopus 로고    scopus 로고
    • Wang, C., Schueler-Furman, O., Andrea, I., London, N., Fleishman, S., Bradley, P., et al. (2007). RosettaDock in CAPRI rounds 6-12. Proteins, doi:10.1002/prot.21684.
  • 37
    • 29144491478 scopus 로고    scopus 로고
    • Molecular basis for bacterial class I release factor methylation by PrmC
    • Graille M., Heurgue-Hamard V., Champ S., Mora L., Scrima N., Ulryck N., et al. Molecular basis for bacterial class I release factor methylation by PrmC. Mol. Cell 20 (2005) 917-927
    • (2005) Mol. Cell , vol.20 , pp. 917-927
    • Graille, M.1    Heurgue-Hamard, V.2    Champ, S.3    Mora, L.4    Scrima, N.5    Ulryck, N.6
  • 38
    • 3042513877 scopus 로고    scopus 로고
    • Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase
    • Yang Z., Shipman L., Zhang M., Anton B.P., Roberts R.J., and Cheng X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J. Mol. Biol. 340 (2004) 695-706
    • (2004) J. Mol. Biol. , vol.340 , pp. 695-706
    • Yang, Z.1    Shipman, L.2    Zhang, M.3    Anton, B.P.4    Roberts, R.J.5    Cheng, X.6
  • 40
    • 13844322130 scopus 로고    scopus 로고
    • Structure, orientation, and conformational changes in transmembrane domains of multidrug transporters
    • Vigano C., Manciu L., and Ruysschaert J.M. Structure, orientation, and conformational changes in transmembrane domains of multidrug transporters. Acc. Chem. Res. 38 (2005) 117-126
    • (2005) Acc. Chem. Res. , vol.38 , pp. 117-126
    • Vigano, C.1    Manciu, L.2    Ruysschaert, J.M.3
  • 41
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin A.M. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 16 (2006) 194-200
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 194-200
    • Bonvin, A.M.1
  • 42
    • 0035427398 scopus 로고    scopus 로고
    • Protein flexibility predictions using graph theory
    • Jacobs D.J., Rader A.J., Kuhn L.A., and Thorpe M.F. Protein flexibility predictions using graph theory. Proteins 44 (2001) 150-165
    • (2001) Proteins , vol.44 , pp. 150-165
    • Jacobs, D.J.1    Rader, A.J.2    Kuhn, L.A.3    Thorpe, M.F.4
  • 43
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar I., and Rader A.J. Coarse-grained normal mode analysis in structural biology. Curr. Opin. Struct. Biol. 15 (2005) 586-592
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 44
    • 0033810049 scopus 로고    scopus 로고
    • Modeling of loops in protein structures
    • Fiser A., Do R.K., and Sali A. Modeling of loops in protein structures. Protein Sci. 9 (2000) 1753-1773
    • (2000) Protein Sci. , vol.9 , pp. 1753-1773
    • Fiser, A.1    Do, R.K.2    Sali, A.3
  • 45
    • 21644487998 scopus 로고    scopus 로고
    • The targets of CAPRI rounds 3-5
    • Janin J. The targets of CAPRI rounds 3-5. Proteins 60 (2005) 170-175
    • (2005) Proteins , vol.60 , pp. 170-175
    • Janin, J.1
  • 48
    • 27344449197 scopus 로고    scopus 로고
    • Progress in modeling of protein structures and interactions
    • Schueler-Furman O., Wang C., Bradley P., Misura K., and Baker D. Progress in modeling of protein structures and interactions. Science 310 (2005) 638-642
    • (2005) Science , vol.310 , pp. 638-642
    • Schueler-Furman, O.1    Wang, C.2    Bradley, P.3    Misura, K.4    Baker, D.5
  • 49
    • 14644438345 scopus 로고    scopus 로고
    • Progress and challenges in high-resolution refinement of protein structure models
    • Misura K.M., and Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 59 (2005) 15-29
    • (2005) Proteins , vol.59 , pp. 15-29
    • Misura, K.M.1    Baker, D.2


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