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Volumn 76, Issue 2, 2009, Pages 309-316

Refining near-native protein-protein docking decoys by local resampling and energy minimization

Author keywords

Docking structure refinement; Energy score; Local resampling

Indexed keywords

DOCKING PROTEIN;

EID: 67650236888     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22343     Document Type: Article
Times cited : (12)

References (35)
  • 1
    • 13844291273 scopus 로고    scopus 로고
    • Protein refinement: A new challenge for CASP in its 10th anniversary
    • Valencia A. Protein refinement: A new challenge for CASP in its 10th anniversary. Bioinformatics 2005;21:277-277.
    • (2005) Bioinformatics , vol.21 , pp. 277-277
    • Valencia, A.1
  • 2
    • 14644438345 scopus 로고    scopus 로고
    • Progress and challenges in high-resolution refinement of protein structure models
    • Misura KM, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins 2005;59:15-29.
    • (2005) Proteins , vol.59 , pp. 15-29
    • Misura, K.M.1    Baker, D.2
  • 3
    • 2442676589 scopus 로고    scopus 로고
    • Automated structure prediction of weakly homologous proteins on a genomic scale
    • Zhang Y, Skolnick J. Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci USA 2004;101:7594-7599.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 7594-7599
    • Zhang, Y.1    Skolnick, J.2
  • 5
    • 0347481194 scopus 로고    scopus 로고
    • Application of statistical potentials to protein structure refinement from low resolution ab initio models
    • Lu H, Skolnick J. Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers 2003;70:575-584.
    • (2003) Biopolymers , vol.70 , pp. 575-584
    • Lu, H.1    Skolnick, J.2
  • 6
    • 0347994106 scopus 로고    scopus 로고
    • Refinement of homology-based protein structures by molecular dynamics simulation techniques
    • Fan H, Mark AE. Refinement of homology-based protein structures by molecular dynamics simulation techniques. Protein Sci 2004;13:211-220.
    • (2004) Protein Sci , vol.13 , pp. 211-220
    • Fan, H.1    Mark, A.E.2
  • 7
    • 17744387920 scopus 로고    scopus 로고
    • All are not equal: A benchmark of different homology modeling programs
    • Wallner B, Elofsson A. All are not equal: a benchmark of different homology modeling programs. Protein Sci 2005;14:1315-1327.
    • (2005) Protein Sci , vol.14 , pp. 1315-1327
    • Wallner, B.1    Elofsson, A.2
  • 8
    • 33645792604 scopus 로고    scopus 로고
    • Physically realistic homology models built with ROSETTA can be more accurate than their templates
    • Misura KMS, Chivian D, Rohl CA, Kim DE, Baker D. Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proc Natl Acad Sci USA 2006;103:5361-5366.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 5361-5366
    • Misura, K.M.S.1    Chivian, D.2    Rohl, C.A.3    Kim, D.E.4    Baker, D.5
  • 9
    • 33749037718 scopus 로고    scopus 로고
    • Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials and clustering
    • Zhu J, Xie L, Honig B. Structural refinement of protein segments containing secondary structure elements: Local sampling, knowledge-based potentials and clustering. Proteins 2006;65:463-479.
    • (2006) Proteins , vol.65 , pp. 463-479
    • Zhu, J.1    Xie, L.2    Honig, B.3
  • 10
    • 33847673583 scopus 로고    scopus 로고
    • Near-native structure refinement using in vacuo energy minimization
    • Summa CM, Levitt M. Near-native structure refinement using in vacuo energy minimization. Proc Natl Acad Sci USA 2007;104:3177-3182.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 3177-3182
    • Summa, C.M.1    Levitt, M.2
  • 11
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen J, Charles L. Brooks I. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins 2007;67:922-930.
    • (2007) Proteins , vol.67 , pp. 922-930
    • Chen, J.1    Charles, L.2    Brooks, I.3
  • 12
    • 0029019869 scopus 로고
    • A continuum model for protein-protein interactions: Application to the docking problem
    • Jackson RM, Sternberg MJE. A continuum model for protein-protein interactions: application to the docking problem. J Mol Biol 1995;250:258-275.
    • (1995) J Mol Biol , vol.250 , pp. 258-275
    • Jackson, R.M.1    Sternberg, M.J.E.2
  • 13
    • 0029933286 scopus 로고    scopus 로고
    • Prediction of protein complexes using empirical free energy functions
    • Weng Z, Vajda S, Delisi C. Prediction of protein complexes using empirical free energy functions. Protein Sci 1996;5:614-626.
    • (1996) Protein Sci , vol.5 , pp. 614-626
    • Weng, Z.1    Vajda, S.2    Delisi, C.3
  • 14
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • Smith GR, Sternberg MJE. Prediction of protein-protein interactions by docking methods. Curr Opin Struct Biol 2002;12:28-35.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.E.2
  • 15
    • 0036108486 scopus 로고    scopus 로고
    • Protein-protein docking with multiple residue conformations and residue substitutions
    • Lorber DM, Udo MK, Shoichet BK. Protein-protein docking with multiple residue conformations and residue substitutions. Protein Sci 2002;11:1393-1408.
    • (2002) Protein Sci , vol.11 , pp. 1393-1408
    • Lorber, D.M.1    Udo, M.K.2    Shoichet, B.K.3
  • 16
    • 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
  • 17
    • 0242299200 scopus 로고    scopus 로고
    • RDOCK: Refinement of rigid-body protein docking predictions
    • Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
    • (2003) Proteins , vol.53 , pp. 693-707
    • Li, L.1    Chen, R.2    Weng, Z.3
  • 18
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 19
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid body displacement and side chain conformations
    • Gray J, Moughan S, Wang C, Schueler-Furman O, Kuhlman B, Rohl C, 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.1    Moughan, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.6    Baker, D.7
  • 20
    • 21644489506 scopus 로고    scopus 로고
    • CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock
    • Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock. Proteins 2005;60:181-186.
    • (2005) Proteins , vol.60 , pp. 181-186
    • Daily, M.D.1    Masica, D.2    Sivasubramanian, A.3    Somarouthu, S.4    Gray, J.J.5
  • 21
    • 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
  • 22
    • 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, 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    Berrondo, M.4    Gray, J.J.5
  • 24
    • 21644440105 scopus 로고    scopus 로고
    • Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI
    • Carter P, Lesk VI, Islam SA, Sternberg MJ. Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 2005;60:281-288.
    • (2005) Proteins , vol.60 , pp. 281-288
    • Carter, P.1    Lesk, V.I.2    Islam, S.A.3    Sternberg, M.J.4
  • 25
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998;276:265-285.
    • (1998) J Mol Biol , vol.276 , pp. 265-285
    • Jackson, R.M.1    Gabb, H.A.2    Sternberg, M.J.3
  • 26
    • 33847317318 scopus 로고    scopus 로고
    • Inherent limitations in protein-protein docking procedures
    • Kowalsman N, Eisenstein M. Inherent limitations in protein-protein docking procedures. Bioinformatics 2007;23:421-426.
    • (2007) Bioinformatics , vol.23 , pp. 421-426
    • Kowalsman, N.1    Eisenstein, M.2
  • 27
    • 34548811419 scopus 로고    scopus 로고
    • A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys
    • Liang S, Liu S, Zhang C, Zhou Y. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys. Proteins 2007;69:244-253.
    • (2007) Proteins , vol.69 , pp. 244-253
    • Liang, S.1    Liu, S.2    Zhang, C.3    Zhou, Y.4
  • 28
    • 0035845563 scopus 로고    scopus 로고
    • Protein docking along smooth association pathways
    • Camacho CJ, Vajda S. Protein docking along smooth association pathways. Proc Natl Acad Sci USA 2001;98:10636-10641.
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 10636-10641
    • Camacho, C.J.1    Vajda, S.2
  • 29
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: Reranking protein docking predictions with an optimized energy function
    • Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 30
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • Zhou H, Zhou Y. Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci 2002;11:2714-2726.
    • (2002) Protein Sci , vol.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 31
    • 2642524483 scopus 로고    scopus 로고
    • A physical reference state unifies the structure-derived potential of mean force for protein folding and binding
    • Liu S, Zhang C, Zhou H, Zhou Y. A physical reference state unifies the structure-derived potential of mean force for protein folding and binding. Proteins 2004;56:93-101.
    • (2004) Proteins , vol.56 , pp. 93-101
    • Liu, S.1    Zhang, C.2    Zhou, H.3    Zhou, Y.4
  • 32
    • 21644446565 scopus 로고    scopus 로고
    • Docking prediction using biological information, ZDOCK sampling technique and clusterization guided by the DFIRE statistical energy function
    • Zhang C, Liu S, Zhou Y. Docking prediction using biological information, ZDOCK sampling technique and clusterization guided by the DFIRE statistical energy function. Proteins 2005;60:314-318.
    • (2005) Proteins , vol.60 , pp. 314-318
    • Zhang, C.1    Liu, S.2    Zhou, Y.3
  • 34
    • 84986512474 scopus 로고    scopus 로고
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
    • Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 1983;4:187-217.
  • 35
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction with an empirical scoring function
    • Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction with an empirical scoring function. Nucleic Acids Res 2006;34:3698-3707.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4


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