메뉴 건너뛰기




Volumn 19, Issue 8, 2014, Pages 1081-1096

Search strategies and evaluation in protein-protein docking: Principles, advances and challenges

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN; PROTEIN BINDING;

EID: 84906324850     PISSN: 13596446     EISSN: 18785832     Source Type: Journal    
DOI: 10.1016/j.drudis.2014.02.005     Document Type: Review
Times cited : (132)

References (165)
  • 2
    • 36349010138 scopus 로고    scopus 로고
    • Protein interactions and disease: Computational approaches to uncover the etiology of diseases
    • M.G. Kann Protein interactions and disease: computational approaches to uncover the etiology of diseases Brief. Bioinform. 8 2007 333 346
    • (2007) Brief. Bioinform. , vol.8 , pp. 333-346
    • Kann, M.G.1
  • 3
    • 3142781225 scopus 로고    scopus 로고
    • Small-molecule inhibitors of protein-protein interactions: Progressing towards the dream
    • M.R. Arkin, and J.A. Wells Small-molecule inhibitors of protein-protein interactions: progressing towards the dream Nat. Rev. Drug Discov. 3 2004 301 317
    • (2004) Nat. Rev. Drug Discov. , vol.3 , pp. 301-317
    • Arkin, M.R.1    Wells, J.A.2
  • 4
    • 58849145512 scopus 로고    scopus 로고
    • Predicting druggable binding sites at the protein-protein interface
    • J.C. Fuller et al. Predicting druggable binding sites at the protein-protein interface Drug Discov. Today 14 2009 155 161
    • (2009) Drug Discov. Today , vol.14 , pp. 155-161
    • Fuller, J.C.1
  • 5
    • 84866354446 scopus 로고    scopus 로고
    • Protein-protein docking and hot-spot prediction for drug discovery
    • S. Grosdidier, and J. Fernandez-Recio Protein-protein docking and hot-spot prediction for drug discovery Curr. Pharm. Des. 18 2012 4607 4618
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 4607-4618
    • Grosdidier, S.1    Fernandez-Recio, J.2
  • 6
    • 84857733776 scopus 로고    scopus 로고
    • Computational drug design targeting protein-protein interactions
    • R.J. Bienstock Computational drug design targeting protein-protein interactions Curr. Pharm. Des. 18 2012 1240 1254
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 1240-1254
    • Bienstock, R.J.1
  • 7
    • 84888844161 scopus 로고    scopus 로고
    • Computational design of protein-protein interactions
    • G. Schreiber, and S.J. Fleishman Computational design of protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 903 910
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 903-910
    • Schreiber, G.1    Fleishman, S.J.2
  • 8
    • 61449145992 scopus 로고    scopus 로고
    • Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach
    • S.-Y. Huang et al. Molecular modeling of the heterodimer of human CFTR's nucleotide-binding domains using a protein-protein docking approach J. Mol. Graph. Model. 27 2009 822 828
    • (2009) J. Mol. Graph. Model. , vol.27 , pp. 822-828
    • Huang, S.-Y.1
  • 9
    • 78649873403 scopus 로고    scopus 로고
    • Ion sensing in the RCK1 domain of BK channels
    • G. Zhang et al. Ion sensing in the RCK1 domain of BK channels Proc. Natl. Acad. Sci. U. S. A. 107 2010 18700 18705
    • (2010) Proc. Natl. Acad. Sci. U. S. A. , vol.107 , pp. 18700-18705
    • Zhang, G.1
  • 10
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • H.M. Berman et al. The Protein Data Bank Nucleic Acids Res. 28 2000 235 242
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 11
    • 78149422216 scopus 로고    scopus 로고
    • Protein-protein docking tested in blind predictions: The CAPRI experiment
    • J. Janin Protein-protein docking tested in blind predictions: the CAPRI experiment Mol. Biosyst. 6 2010 2351 2362
    • (2010) Mol. Biosyst. , vol.6 , pp. 2351-2362
    • Janin, J.1
  • 12
    • 0018165127 scopus 로고
    • Computer analysis of protein-protein interaction
    • S.J. Wodak, and J. Janin Computer analysis of protein-protein interaction J. Mol. Biol. 124 1978 323 342
    • (1978) J. Mol. Biol. , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 13
    • 0036468385 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions by docking methods
    • G.R. Smith, and M.J. Sternberg Prediction of protein-protein interactions by docking methods Curr. Opin. Struct. Biol. 12 2002 28 35
    • (2002) Curr. Opin. Struct. Biol. , vol.12 , pp. 28-35
    • Smith, G.R.1    Sternberg, M.J.2
  • 14
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • J.J. Gray High-resolution protein-protein docking Curr. Opin. Struct. Biol. 16 2006 183 193
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 15
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • A.M. Bonvin 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
  • 16
    • 52249122794 scopus 로고    scopus 로고
    • Principles of flexible protein-protein docking
    • N. Andrusier et al. Principles of flexible protein-protein docking Proteins 73 2008 271 289
    • (2008) Proteins , vol.73 , pp. 271-289
    • Andrusier, N.1
  • 17
    • 77951297973 scopus 로고    scopus 로고
    • Accounting for conformational changes during protein-protein docking
    • M. Zacharias Accounting for conformational changes during protein-protein docking Curr. Opin. Struct. Biol. 20 2010 180 186
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 180-186
    • Zacharias, M.1
  • 18
    • 41949111630 scopus 로고    scopus 로고
    • Recent progress and future directions in protein-protein docking
    • D.W. Ritchie Recent progress and future directions in protein-protein docking Curr. Protein Pept. Sci. 9 2008 1 15
    • (2008) Curr. Protein Pept. Sci. , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 19
    • 64549106038 scopus 로고    scopus 로고
    • Convergence and combination of methods in protein-protein docking
    • S. Vajda, and D. Kozakov Convergence and combination of methods in protein-protein docking Curr. Opin. Struct. Biol. 19 2009 164 170
    • (2009) Curr. Opin. Struct. Biol. , vol.19 , pp. 164-170
    • Vajda, S.1    Kozakov, D.2
  • 20
    • 84885074179 scopus 로고    scopus 로고
    • Sampling and scoring: A marriage made in heaven
    • S. Vajda et al. Sampling and scoring: a marriage made in heaven Proteins 81 2013 1874 1884
    • (2013) Proteins , vol.81 , pp. 1874-1884
    • Vajda, S.1
  • 21
    • 84888818673 scopus 로고    scopus 로고
    • Scoring functions for protein-protein interactions
    • I.H. Moal et al. Scoring functions for protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 862 867
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 862-867
    • Moal, I.H.1
  • 22
    • 84878552481 scopus 로고    scopus 로고
    • Low-resolution structural modeling of protein interactome
    • I.A. Vakser Low-resolution structural modeling of protein interactome Curr. Opin. Struct. Biol. 23 2013 198 205
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 198-205
    • Vakser, I.A.1
  • 23
    • 77957899529 scopus 로고    scopus 로고
    • Advances and challenges in protein-ligand docking
    • S-Y. Huang, and X. Zou Advances and challenges in protein-ligand docking Int. J. Mol. Sci. 11 2010 3016 3034
    • (2010) Int. J. Mol. Sci. , vol.11 , pp. 3016-3034
    • Huang, S.-Y.1    Zou, X.2
  • 24
    • 77957898063 scopus 로고    scopus 로고
    • Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
    • S-Y. Huang et al. Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions Phys. Chem. Chem. Phys. 12 2010 12899 12908
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 12899-12908
    • Huang, S.-Y.1
  • 25
    • 0026572775 scopus 로고
    • Molecular surface recognition: Determination of geometric fit between proteins and their ligands by correlation techniques
    • E. Katchalski-Katzir et al. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques Proc. Natl. Acad. Sci. U. S. A. 89 1992 2195 2199
    • (1992) Proc. Natl. Acad. Sci. U. S. A. , vol.89 , pp. 2195-2199
    • Katchalski-Katzir, E.1
  • 26
    • 0031565730 scopus 로고    scopus 로고
    • Modelling protein docking using shape complementarity, electrostatics and biochemical information
    • H.A. Gabb et al. Modelling protein docking using shape complementarity, electrostatics and biochemical information J. Mol. Biol. 272 1997 106 120
    • (1997) J. Mol. Biol. , vol.272 , pp. 106-120
    • Gabb, H.A.1
  • 27
    • 0031296607 scopus 로고    scopus 로고
    • Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
    • I.A. Vakser Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex Proteins 29 Suppl. 1 1997 226 230
    • (1997) Proteins , vol.29 , Issue.SUPPL. 1 , pp. 226-230
    • Vakser, I.A.1
  • 28
    • 0035040480 scopus 로고    scopus 로고
    • Protein docking using continuum electrostatics and geometric fit
    • J.G. Mandell et al. Protein docking using continuum electrostatics and geometric fit Protein Eng. 14 2001 105 113
    • (2001) Protein Eng. , vol.14 , pp. 105-113
    • Mandell, J.G.1
  • 29
    • 84879461612 scopus 로고    scopus 로고
    • DOT2: Macromolecular docking with improved biophysical models
    • V.A. Roberts et al. DOT2: macromolecular docking with improved biophysical models J. Comput. Chem. 34 2013 1743 1758
    • (2013) J. Comput. Chem. , vol.34 , pp. 1743-1758
    • Roberts, V.A.1
  • 30
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • R. Chen, and Z.P. Weng Docking unbound proteins using shape complementarity, desolvation, and electrostatics Proteins 47 2002 281 294
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.P.2
  • 31
    • 0038185277 scopus 로고    scopus 로고
    • A novel shape complementarity scoring function for protein-protein docking
    • R. Chen, and Z. Weng A novel shape complementarity scoring function for protein-protein docking Proteins 51 2003 397 408
    • (2003) Proteins , vol.51 , pp. 397-408
    • Chen, R.1    Weng, Z.2
  • 32
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: An initial-stage protein docking algorithm
    • R. Chen et al. ZDOCK: an initial-stage protein docking algorithm Proteins 52 2003 80 87
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1
  • 33
    • 35449008122 scopus 로고    scopus 로고
    • Integrating statistical pair potentials into protein complex prediction
    • J. Mintseris et al. Integrating statistical pair potentials into protein complex prediction Proteins 69 2007 511 520
    • (2007) Proteins , vol.69 , pp. 511-520
    • Mintseris, J.1
  • 34
    • 80052903046 scopus 로고    scopus 로고
    • Accelerating protein docking in ZDOCK using an advanced 3D convolution library
    • B.G. Pierce et al. Accelerating protein docking in ZDOCK using an advanced 3D convolution library PLoS ONE 6 2011 e24657
    • (2011) PLoS ONE , vol.6 , pp. 24657
    • Pierce, B.G.1
  • 35
    • 0036180566 scopus 로고    scopus 로고
    • Electrostatics in protein-protein docking
    • A. Heifetz et al. Electrostatics in protein-protein docking Protein Sci. 11 2002 571 587
    • (2002) Protein Sci. , vol.11 , pp. 571-587
    • Heifetz, A.1
  • 36
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: An FFT-based protein docking program with pairwise potentials
    • D. Kozakov et al. PIPER: an FFT-based protein docking program with pairwise potentials Proteins 65 2006 392 406
    • (2006) Proteins , vol.65 , pp. 392-406
    • Kozakov, D.1
  • 37
  • 38
    • 79959698679 scopus 로고    scopus 로고
    • SDOCK: A global protein-protein docking program using stepwise force-field potentials
    • C. Zhang, and L. Lai SDOCK: a global protein-protein docking program using stepwise force-field potentials J. Comput. Chem. 32 2011 2598 2612
    • (2011) J. Comput. Chem. , vol.32 , pp. 2598-2612
    • Zhang, C.1    Lai, L.2
  • 39
    • 84866454213 scopus 로고    scopus 로고
    • Cell-Dock: High-performance protein-protein docking
    • C. Pons et al. Cell-Dock: high-performance protein-protein docking Bioinformatics 28 2012 2394 2396
    • (2012) Bioinformatics , vol.28 , pp. 2394-2396
    • Pons, C.1
  • 40
    • 0038187616 scopus 로고    scopus 로고
    • Weighted geometric docking: Incorporating external information in the rotation-translation scan
    • E. Ben-Zeev, and M. Eisenstein Weighted geometric docking: incorporating external information in the rotation-translation scan Proteins 52 2003 24 27
    • (2003) Proteins , vol.52 , pp. 24-27
    • Ben-Zeev, E.1    Eisenstein, M.2
  • 41
    • 79251557484 scopus 로고    scopus 로고
    • ASPDock: Protein-protein docking algorithm using atomic solvation parameters model
    • L. Li et al. ASPDock: protein-protein docking algorithm using atomic solvation parameters model BMC Bioinformatics 12 2011 36
    • (2011) BMC Bioinformatics , vol.12 , pp. 36
    • Li, L.1
  • 42
    • 2642518000 scopus 로고    scopus 로고
    • Hydrophobic complementarity in protein-protein docking
    • A. Berchanski et al. Hydrophobic complementarity in protein-protein docking Proteins 56 2004 130 142
    • (2004) Proteins , vol.56 , pp. 130-142
    • Berchanski, A.1
  • 43
    • 21644450650 scopus 로고    scopus 로고
    • Modeling oligomers with Cn or Dn symmetry: Application to CAPRI target 10
    • A. Berchanski et al. Modeling oligomers with Cn or Dn symmetry: application to CAPRI target 10 Proteins 60 2005 202 206
    • (2005) Proteins , vol.60 , pp. 202-206
    • Berchanski, A.1
  • 44
    • 17444385658 scopus 로고    scopus 로고
    • M-ZDOCK: A grid-based approach for Cn symmetric multimer docking
    • B. Pierce et al. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking Bioinformatics 21 2005 1472 1478
    • (2005) Bioinformatics , vol.21 , pp. 1472-1478
    • Pierce, B.1
  • 45
    • 70349882144 scopus 로고    scopus 로고
    • FRODOCK: A new approach for fast rotational protein-protein docking
    • J.I. Garzon et al. FRODOCK: a new approach for fast rotational protein-protein docking Bioinformatics 25 2009 2544 2551
    • (2009) Bioinformatics , vol.25 , pp. 2544-2551
    • Garzon, J.I.1
  • 46
    • 0034193510 scopus 로고    scopus 로고
    • Protein docking using spherical polar Fourier correlations
    • D.W. Ritchie, and G.J. Kemp Protein docking using spherical polar Fourier correlations Proteins 39 2000 178 194
    • (2000) Proteins , vol.39 , pp. 178-194
    • Ritchie, D.W.1    Kemp, G.J.2
  • 47
    • 50549092426 scopus 로고    scopus 로고
    • Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions
    • D.W. Ritchie et al. Accelerating and focusing protein-protein docking correlations using multi-dimensional rotational FFT generating functions Bioinformatics 24 2008 1865 1873
    • (2008) Bioinformatics , vol.24 , pp. 1865-1873
    • Ritchie, D.W.1
  • 48
    • 77957242885 scopus 로고    scopus 로고
    • Ultra-fast FFT protein docking on graphics processors
    • D.W. Ritchie, and V. Venkatraman Ultra-fast FFT protein docking on graphics processors Bioinformatics 26 2010 2398 2405
    • (2010) Bioinformatics , vol.26 , pp. 2398-2405
    • Ritchie, D.W.1    Venkatraman, V.2
  • 49
    • 0026310932 scopus 로고
    • 'Soft docking': Matching of molecular surface cubes
    • F. Jiang, and S.H. Kim 'Soft docking': matching of molecular surface cubes J. Mol. Biol. 219 1991 79 102
    • (1991) J. Mol. Biol. , vol.219 , pp. 79-102
    • Jiang, F.1    Kim, S.H.2
  • 50
    • 0034212826 scopus 로고    scopus 로고
    • BiGGER: A new (soft) docking algorithm for predicting protein interactions
    • P.N. Palma et al. BiGGER: a new (soft) docking algorithm for predicting protein interactions Proteins 39 2000 372 384
    • (2000) Proteins , vol.39 , pp. 372-384
    • Palma, P.N.1
  • 51
    • 36749078011 scopus 로고    scopus 로고
    • The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation
    • G. Terashi et al. The SKE-DOCK server and human teams based on a combined method of shape complementarity and free energy estimation Proteins 69 2007 866 872
    • (2007) Proteins , vol.69 , pp. 866-872
    • Terashi, G.1
  • 52
    • 0020491251 scopus 로고
    • A geometric approach to macromolecule-ligand interactions
    • I.D. Kuntz et al. A geometric approach to macromolecule-ligand interactions J. Mol. Biol. 161 1982 269 288
    • (1982) J. Mol. Biol. , vol.161 , pp. 269-288
    • Kuntz, I.D.1
  • 53
    • 84956979675 scopus 로고    scopus 로고
    • Efficient unbound docking of rigid molecules
    • D. Duhovny et al. Efficient unbound docking of rigid molecules Lect. Notes Comp. Sci. 2452 2002 185 200
    • (2002) Lect. Notes Comp. Sci. , vol.2452 , pp. 185-200
    • Duhovny, D.1
  • 54
    • 21644476468 scopus 로고    scopus 로고
    • PatchDock and SymmDock: Servers for rigid and symmetric docking
    • D. Schneidman-Duhovny et al. PatchDock and SymmDock: servers for rigid and symmetric docking Nucleic Acids Res. 33 2005 W363 W367
    • (2005) Nucleic Acids Res. , vol.33
    • Schneidman-Duhovny, D.1
  • 55
    • 74049092313 scopus 로고    scopus 로고
    • Protein-protein docking using region-based 3D Zernike descriptors
    • V. Venkatraman et al. Protein-protein docking using region-based 3D Zernike descriptors BMC Bioinformatics 10 2009 407
    • (2009) BMC Bioinformatics , vol.10 , pp. 407
    • Venkatraman, V.1
  • 56
    • 84862196732 scopus 로고    scopus 로고
    • Multi-LZerD: Multiple protein docking for asymmetric complexes
    • J. Esquivel-Rodriguez et al. Multi-LZerD: multiple protein docking for asymmetric complexes Proteins 80 2012 1818 1833
    • (2012) Proteins , vol.80 , pp. 1818-1833
    • Esquivel-Rodriguez, J.1
  • 57
    • 0035400404 scopus 로고    scopus 로고
    • Protein docking using a genetic algorithm
    • E.J. Gardiner et al. Protein docking using a genetic algorithm Proteins 44 2001 44 56
    • (2001) Proteins , vol.44 , pp. 44-56
    • Gardiner, E.J.1
  • 58
    • 0025785057 scopus 로고
    • Protein docking and complementarity
    • B.K. Shoichet, and I.D. Kuntz Protein docking and complementarity J. Mol. Biol. 221 1991 327 346
    • (1991) J. Mol. Biol. , vol.221 , pp. 327-346
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 59
    • 0030090466 scopus 로고    scopus 로고
    • Predicting the structure of protein complexes: A step in the right direction
    • B.K. Shoichet, and I.D. Kuntz Predicting the structure of protein complexes: a step in the right direction Chem. Biol. 3 1996 151 156
    • (1996) Chem. Biol. , vol.3 , pp. 151-156
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 60
    • 0036108486 scopus 로고    scopus 로고
    • Protein-protein docking with multiple residue conformations and residue substitutions
    • D.M. Lorber et al. Protein-protein docking with multiple residue conformations and residue substitutions Protein Sci. 11 2002 1393 1408
    • (2002) Protein Sci. , vol.11 , pp. 1393-1408
    • Lorber, D.M.1
  • 61
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • J.J. Gray et al. 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
  • 62
    • 34548861782 scopus 로고    scopus 로고
    • Protein-protein docking with backbone flexibility
    • C. Wang et al. Protein-protein docking with backbone flexibility J. Mol. Biol. 373 2007 503 519
    • (2007) J. Mol. Biol. , vol.373 , pp. 503-519
    • Wang, C.1
  • 63
    • 48449094112 scopus 로고    scopus 로고
    • Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles
    • S. Chaudhury, and J.J. Gray Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles J. Mol. Biol. 381 2008 1068 1087
    • (2008) J. Mol. Biol. , vol.381 , pp. 1068-1087
    • Chaudhury, S.1    Gray, J.J.2
  • 64
    • 79961012919 scopus 로고    scopus 로고
    • Benchmarking and analysis of protein docking performance in Rosetta v3.2
    • S. Chaudhury et al. Benchmarking and analysis of protein docking performance in Rosetta v3.2 PLoS ONE 6 2011 e22477
    • (2011) PLoS ONE , vol.6 , pp. 22477
    • Chaudhury, S.1
  • 65
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • M. Zacharias Protein-protein docking with a reduced protein model accounting for side-chain flexibility Protein Sci. 12 2003 1271 1282
    • (2003) Protein Sci. , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 66
    • 21644435306 scopus 로고    scopus 로고
    • ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
    • M. Zacharias ATTRACT: protein-protein docking in CAPRI using a reduced protein model Proteins 60 2005 252 256
    • (2005) Proteins , vol.60 , pp. 252-256
    • Zacharias, M.1
  • 67
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • K. Bastard et al. Accounting for loop flexibility during protein-protein docking Proteins 62 2006 956 969
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1
  • 68
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
    • C. Dominguez et al. 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
  • 69
    • 36748998784 scopus 로고    scopus 로고
    • HADDOCK versus HADDOCK: New features and performance of HADDOCK2.0 on the CAPRI targets
    • S.J. de Vries et al. HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets Proteins 69 2007 726 733
    • (2007) Proteins , vol.69 , pp. 726-733
    • De Vries, S.J.1
  • 70
    • 84986522918 scopus 로고
    • ICM: A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
    • R. Abagyan et al. 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
  • 71
    • 17344380633 scopus 로고    scopus 로고
    • ICM-DISCO docking by global energy optimization with fully flexible side-chains
    • J. Fernandez-Recio et al. ICM-DISCO docking by global energy optimization with fully flexible side-chains Proteins 52 2003 113 117
    • (2003) Proteins , vol.52 , pp. 113-117
    • Fernandez-Recio, J.1
  • 72
    • 77958133774 scopus 로고    scopus 로고
    • SwarmDock and the use of normal modes in protein-protein docking
    • I.H. Moal, and P.A. Bates SwarmDock and the use of normal modes in protein-protein docking Int. J. Mol. Sci. 11 2010 3623 3648
    • (2010) Int. J. Mol. Sci. , vol.11 , pp. 3623-3648
    • Moal, I.H.1    Bates, P.A.2
  • 73
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function
    • G.M. Morris et al. Automated docking using a Lamarckian genetic algorithm and empirical binding free energy function J. Comput. Chem. 19 1998 1639 1662
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1
  • 74
    • 55849144771 scopus 로고    scopus 로고
    • Emergence of symmetry in homooligomeric biological assemblies
    • I. Andre et al. Emergence of symmetry in homooligomeric biological assemblies Proc. Natl. Acad. Sci. U. S. A. 105 2008 16148 16152
    • (2008) Proc. Natl. Acad. Sci. U. S. A. , vol.105 , pp. 16148-16152
    • Andre, I.1
  • 75
    • 66149165880 scopus 로고    scopus 로고
    • PTools: An opensource molecular docking library
    • A. Saladin et al. PTools: an opensource molecular docking library BMC Struct. Biol. 9 2009 27
    • (2009) BMC Struct. Biol. , vol.9 , pp. 27
    • Saladin, A.1
  • 76
    • 0038359614 scopus 로고    scopus 로고
    • CAPRI: A critical assessment of predicted interactions
    • J. Janin et al. CAPRI: a critical assessment of predicted interactions Proteins 52 2003 2 9
    • (2003) Proteins , vol.52 , pp. 2-9
    • Janin, J.1
  • 77
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • R. Mendez et al. 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
  • 78
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd edition
    • M.F. Lensink et al. Docking and scoring protein complexes: CAPRI 3rd edition Proteins 69 2007 704 718
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1
  • 79
    • 77957948556 scopus 로고    scopus 로고
    • Blind predictions of protein interfaces by docking calculations in CAPRI
    • M.F. Lensink, and S.J. Wodak Blind predictions of protein interfaces by docking calculations in CAPRI Proteins 78 2010 3085 3095
    • (2010) Proteins , vol.78 , pp. 3085-3095
    • Lensink, M.F.1    Wodak, S.J.2
  • 80
    • 84888289172 scopus 로고    scopus 로고
    • Docking, scoring and affinity prediction in CAPRI
    • M.F. Lensink, and S.J. Wodak Docking, scoring and affinity prediction in CAPRI Proteins 81 2013 2082 2095
    • (2013) Proteins , vol.81 , pp. 2082-2095
    • Lensink, M.F.1    Wodak, S.J.2
  • 81
    • 0033562633 scopus 로고    scopus 로고
    • Use of pair potentials across protein interfaces in screening predicted docked complexes
    • G. Moont et al. Use of pair potentials across protein interfaces in screening predicted docked complexes Proteins 35 1999 364 373
    • (1999) Proteins , vol.35 , pp. 364-373
    • Moont, G.1
  • 82
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: Reranking protein docking predictions with an optimized energy function
    • B. Pierce, and Z. Weng ZRANK: reranking protein docking predictions with an optimized energy function Proteins 67 2007 1078 1086
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 83
    • 34250882254 scopus 로고    scopus 로고
    • PyDock: Electrostatics and desolvation for effective scoring of rigid-body protein-protein docking
    • T.M. Cheng et al. pyDock: electrostatics and desolvation for effective scoring of rigid-body protein-protein docking Proteins 68 2007 503 515
    • (2007) Proteins , vol.68 , pp. 503-515
    • Cheng, T.M.1
  • 84
    • 34548811419 scopus 로고    scopus 로고
    • A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys
    • S. Liang et al. A simple reference state makes a significant improvement in near-native selections from structurally refined docking decoys Proteins 69 2007 244 253
    • (2007) Proteins , vol.69 , pp. 244-253
    • Liang, S.1
  • 85
    • 58149152509 scopus 로고    scopus 로고
    • DARS (Decoys As the Reference State) potentials for protein-protein docking
    • G.Y. Chuang et al. DARS (Decoys As the Reference State) potentials for protein-protein docking Biophys. J. 95 2008 4217 4227
    • (2008) Biophys. J. , vol.95 , pp. 4217-4227
    • Chuang, G.Y.1
  • 86
    • 79960036791 scopus 로고    scopus 로고
    • DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking
    • S. Liu, and I.A. Vakser DECK: distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking BMC Bioinformatics 12 2011 280
    • (2011) BMC Bioinformatics , vol.12 , pp. 280
    • Liu, S.1    Vakser, I.A.2
  • 87
    • 79952132540 scopus 로고    scopus 로고
    • Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): A new efficient potential for protein-protein docking
    • C. Pons et al. Scoring by intermolecular pairwise propensities of exposed residues (SIPPER): a new efficient potential for protein-protein docking J. Chem. Inf. Model. 51 2011 370 377
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 370-377
    • Pons, C.1
  • 88
    • 77449134208 scopus 로고    scopus 로고
    • PIE-efficient filters and coarse grained potentials for unbound protein-protein docking
    • D.V. Ravikant, and R. Elber PIE-efficient filters and coarse grained potentials for unbound protein-protein docking Proteins 78 2010 400 419
    • (2010) Proteins , vol.78 , pp. 400-419
    • Ravikant, D.V.1    Elber, R.2
  • 89
    • 77957934483 scopus 로고    scopus 로고
    • MDockPP: A hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19
    • S-Y. Huang, and X. Zou MDockPP: a hierarchical approach for protein-protein docking and its application to CAPRI rounds 15-19 Proteins 78 2010 3096 3103
    • (2010) Proteins , vol.78 , pp. 3096-3103
    • Huang, S.-Y.1    Zou, X.2
  • 90
    • 46449084711 scopus 로고    scopus 로고
    • An iterative knowledge-based scoring function for protein-protein recognition
    • S.-Y. Huang, and X. Zou An iterative knowledge-based scoring function for protein-protein recognition Proteins 72 2008 557 579
    • (2008) Proteins , vol.72 , pp. 557-579
    • Huang, S.-Y.1    Zou, X.2
  • 91
    • 84860388898 scopus 로고    scopus 로고
    • Integrating atom-based and residue-based scoring functions for protein-protein docking
    • T. Vreven et al. Integrating atom-based and residue-based scoring functions for protein-protein docking Protein Sci. 20 2011 1576 1586
    • (2011) Protein Sci. , vol.20 , pp. 1576-1586
    • Vreven, T.1
  • 92
    • 84855256224 scopus 로고    scopus 로고
    • Scoring optimisation of unbound protein-protein docking including protein binding site predictions
    • S. Schneider, and M. Zacharias Scoring optimisation of unbound protein-protein docking including protein binding site predictions J. Mol. Recognit. 25 2012 15 23
    • (2012) J. Mol. Recognit. , vol.25 , pp. 15-23
    • Schneider, S.1    Zacharias, M.2
  • 93
    • 84871061224 scopus 로고    scopus 로고
    • Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling
    • M. Zacharias Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling Proteins 81 2013 81 92
    • (2013) Proteins , vol.81 , pp. 81-92
    • Zacharias, M.1
  • 94
    • 84880245822 scopus 로고    scopus 로고
    • InterEvScore: A novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution
    • J. Andreani et al. InterEvScore: a novel coarse-grained interface scoring function using a multi-body statistical potential coupled to evolution Bioinformatics 29 2013 1742 1749
    • (2013) Bioinformatics , vol.29 , pp. 1742-1749
    • Andreani, J.1
  • 95
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • R.M. Jackson et al. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem J. Mol. Biol. 276 1998 265 285
    • (1998) J. Mol. Biol. , vol.276 , pp. 265-285
    • Jackson, R.M.1
  • 96
    • 0038359596 scopus 로고    scopus 로고
    • Successful discrimination of protein interactions
    • C.J. Camacho, and D.W. Gatchell Successful discrimination of protein interactions Proteins 52 2003 92 97
    • (2003) Proteins , vol.52 , pp. 92-97
    • Camacho, C.J.1    Gatchell, D.W.2
  • 97
    • 0242299200 scopus 로고    scopus 로고
    • RDOCK: Refinement of rigid-body protein docking predictions
    • L. Li et al. RDOCK: refinement of rigid-body protein docking predictions Proteins 53 2003 693 707
    • (2003) Proteins , vol.53 , pp. 693-707
    • Li, L.1
  • 98
    • 34548317146 scopus 로고    scopus 로고
    • FireDock: Fast interaction refinement in molecular docking
    • N. Andrusier et al. FireDock: fast interaction refinement in molecular docking Proteins 69 2007 139 159
    • (2007) Proteins , vol.69 , pp. 139-159
    • Andrusier, N.1
  • 99
    • 77951232176 scopus 로고    scopus 로고
    • FiberDock: Flexible induced-fit backbone refinement in molecular docking
    • E. Mashiach et al. FiberDock: flexible induced-fit backbone refinement in molecular docking Proteins 78 2010 1503 1519
    • (2010) Proteins , vol.78 , pp. 1503-1519
    • Mashiach, E.1
  • 100
    • 84864418223 scopus 로고    scopus 로고
    • Flexible protein docking refinement using pose-dependent normal mode analysis
    • V. Venkatraman, and D.W. Ritchie Flexible protein docking refinement using pose-dependent normal mode analysis Proteins 80 2012 2262 2274
    • (2012) Proteins , vol.80 , pp. 2262-2274
    • Venkatraman, V.1    Ritchie, D.W.2
  • 101
    • 36749057349 scopus 로고    scopus 로고
    • Implicit flexibility in protein docking: Cross-docking and local refinement
    • M. Krol et al. Implicit flexibility in protein docking: cross-docking and local refinement Proteins 69 2007 750 757
    • (2007) Proteins , vol.69 , pp. 750-757
    • Krol, M.1
  • 102
    • 36448981368 scopus 로고    scopus 로고
    • Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization
    • S. Lorenzen, and Y. Zhang Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization Protein Sci. 16 2007 2716 2725
    • (2007) Protein Sci. , vol.16 , pp. 2716-2725
    • Lorenzen, S.1    Zhang, Y.2
  • 103
    • 67650236888 scopus 로고    scopus 로고
    • Refining near-native protein-protein docking decoys by local re-sampling and energy minimization
    • S. Liang et al. Refining near-native protein-protein docking decoys by local re-sampling and energy minimization Proteins 76 2009 309 316
    • (2009) Proteins , vol.76 , pp. 309-316
    • Liang, S.1
  • 104
    • 84874791762 scopus 로고    scopus 로고
    • Improving ranking of models for protein complexes with side chain modeling and atomic potentials
    • S. Viswanath et al. Improving ranking of models for protein complexes with side chain modeling and atomic potentials Proteins 81 2013 592 606
    • (2013) Proteins , vol.81 , pp. 592-606
    • Viswanath, S.1
  • 105
    • 55449101982 scopus 로고    scopus 로고
    • Protein docking by the underestimation of free energy funnels in the space of encounter complexes
    • Y. Shen et al. Protein docking by the underestimation of free energy funnels in the space of encounter complexes PLoS Comput. Biol. 4 2008 e1000191
    • (2008) PLoS Comput. Biol. , vol.4 , pp. 1000191
    • Shen, Y.1
  • 106
    • 84878141430 scopus 로고    scopus 로고
    • CyClus: A fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys
    • S. Omori, and A. Kitao CyClus: a fast, comprehensive cylindrical interface approximation clustering/reranking method for rigid-body protein-protein docking decoys Proteins 81 2013 1005 1016
    • (2013) Proteins , vol.81 , pp. 1005-1016
    • Omori, S.1    Kitao, A.2
  • 107
    • 84882901819 scopus 로고    scopus 로고
    • Ranking multiple docking solutions based on the conservation of inter-residue contacts
    • R. Oliva et al. Ranking multiple docking solutions based on the conservation of inter-residue contacts Proteins 81 2013 1571 1584
    • (2013) Proteins , vol.81 , pp. 1571-1584
    • Oliva, R.1
  • 108
    • 36749082073 scopus 로고    scopus 로고
    • A holistic approach to protein docking
    • S. Qin, and H.X. Zhou A holistic approach to protein docking Proteins 69 2007 743 749
    • (2007) Proteins , vol.69 , pp. 743-749
    • Qin, S.1    Zhou, H.X.2
  • 109
    • 34249912111 scopus 로고    scopus 로고
    • Identification of near-native structures by clustering protein docking conformations
    • S. Lorenzen, and Y. Zhang Identification of near-native structures by clustering protein docking conformations Proteins 68 2007 187 194
    • (2007) Proteins , vol.68 , pp. 187-194
    • Lorenzen, S.1    Zhang, Y.2
  • 110
    • 47349119911 scopus 로고    scopus 로고
    • Discrimination of near-native structures in protein-protein docking by testing the stability of local minima
    • D. Kozakov et al. Discrimination of near-native structures in protein-protein docking by testing the stability of local minima Proteins 72 2008 993 1004
    • (2008) Proteins , vol.72 , pp. 993-1004
    • Kozakov, D.1
  • 111
    • 70349459669 scopus 로고    scopus 로고
    • Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models
    • N. Kowalsman, and M. Eisenstein Combining interface core and whole interface descriptors in postscan processing of protein-protein docking models Proteins 77 2009 297 318
    • (2009) Proteins , vol.77 , pp. 297-318
    • Kowalsman, N.1    Eisenstein, M.2
  • 112
    • 33847317318 scopus 로고    scopus 로고
    • Inherent limitations in protein-protein docking procedures
    • N. Kowalsman, and M. Eisenstein Inherent limitations in protein-protein docking procedures Bioinformatics 23 2007 421 426
    • (2007) Bioinformatics , vol.23 , pp. 421-426
    • Kowalsman, N.1    Eisenstein, M.2
  • 113
    • 84891818638 scopus 로고    scopus 로고
    • KBDOCK 2013: A spatial classification of 3D protein domain family interactions
    • A.W. Ghoorah et al. KBDOCK 2013: a spatial classification of 3D protein domain family interactions Nucleic Acids Res. 2014 http://dx.doi.org/10.1093/ nar/gkt1199
    • (2014) Nucleic Acids Res.
    • Ghoorah, A.W.1
  • 114
    • 84885028725 scopus 로고    scopus 로고
    • How to use not-always-reliable binding site information in protein-protein docking prediction
    • L. Li et al. How to use not-always-reliable binding site information in protein-protein docking prediction PLoS ONE 8 2013 e75936
    • (2013) PLoS ONE , vol.8 , pp. 75936
    • Li, L.1
  • 115
    • 0037849892 scopus 로고    scopus 로고
    • Prediction of the unknown: Inspiring experience with the CAPRI experiment
    • E. Ben-Zeev et al. Prediction of the unknown: inspiring experience with the CAPRI experiment Proteins 52 2003 41 46
    • (2003) Proteins , vol.52 , pp. 41-46
    • Ben-Zeev, E.1
  • 116
    • 84874328246 scopus 로고    scopus 로고
    • Exploring angular distance in protein-protein docking algorithms
    • T. Vreven et al. Exploring angular distance in protein-protein docking algorithms PLoS ONE 8 2013 e56645
    • (2013) PLoS ONE , vol.8 , pp. 56645
    • Vreven, T.1
  • 117
    • 84890029384 scopus 로고    scopus 로고
    • Template-based structure modeling of protein-protein interactions
    • A. Szilagyi, and Y. Zhang Template-based structure modeling of protein-protein interactions Curr. Opin. Struct. Biol. 24 2014 10 23
    • (2014) Curr. Opin. Struct. Biol. , vol.24 , pp. 10-23
    • Szilagyi, A.1    Zhang, Y.2
  • 118
    • 84862233055 scopus 로고    scopus 로고
    • Templates are available to model nearly all complexes of structurally characterized proteins
    • P.J. Kundrotas et al. Templates are available to model nearly all complexes of structurally characterized proteins Proc. Natl. Acad. Sci. U. S. A. 109 2012 9438 9441
    • (2012) Proc. Natl. Acad. Sci. U. S. A. , vol.109 , pp. 9438-9441
    • Kundrotas, P.J.1
  • 119
    • 79960164372 scopus 로고    scopus 로고
    • Protein-protein complex structure predictions by multimeric threading and template recombination
    • S. Mukherjee, and Y. Zhang Protein-protein complex structure predictions by multimeric threading and template recombination Structure 19 2011 955 966
    • (2011) Structure , vol.19 , pp. 955-966
    • Mukherjee, S.1    Zhang, Y.2
  • 120
    • 84867881743 scopus 로고    scopus 로고
    • Structure-based prediction of protein-protein interactions on a genome-wide scale
    • Q.C. Zhang et al. Structure-based prediction of protein-protein interactions on a genome-wide scale Nature 490 2012 556 560
    • (2012) Nature , vol.490 , pp. 556-560
    • Zhang, Q.C.1
  • 121
    • 84875464398 scopus 로고    scopus 로고
    • Mapping monomeric threading to protein-protein structure prediction
    • A. Guerler et al. Mapping monomeric threading to protein-protein structure prediction J. Chem. Inf. Model. 53 2013 717 725
    • (2013) J. Chem. Inf. Model. , vol.53 , pp. 717-725
    • Guerler, A.1
  • 122
    • 80052411919 scopus 로고    scopus 로고
    • Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM
    • N. Tuncbag et al. Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM Nat. Protoc. 6 2011 1341 1354
    • (2011) Nat. Protoc. , vol.6 , pp. 1341-1354
    • Tuncbag, N.1
  • 123
    • 80053947029 scopus 로고    scopus 로고
    • Spatial clustering of protein binding sites for template based protein docking
    • A.W. Ghoorah et al. Spatial clustering of protein binding sites for template based protein docking Bioinformatics 27 2011 2820 2827
    • (2011) Bioinformatics , vol.27 , pp. 2820-2827
    • Ghoorah, A.W.1
  • 124
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • S-Y. Huang, and X. Zou Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking Proteins 66 2007 399 421
    • (2007) Proteins , vol.66 , pp. 399-421
    • Huang, S.-Y.1    Zou, X.2
  • 125
    • 84874871709 scopus 로고    scopus 로고
    • A unified conformational selection and induced fit approach to protein-peptide docking
    • M. Trellet et al. A unified conformational selection and induced fit approach to protein-peptide docking PLoS ONE 8 2013 e58769
    • (2013) PLoS ONE , vol.8 , pp. 58769
    • Trellet, M.1
  • 126
    • 84888825453 scopus 로고    scopus 로고
    • Coarse-grain modelling of protein-protein interactions
    • M. Baaden, and S.J. Marrink Coarse-grain modelling of protein-protein interactions Curr. Opin. Struct. Biol. 23 2013 878 886
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 878-886
    • Baaden, M.1    Marrink, S.J.2
  • 127
    • 84872126088 scopus 로고    scopus 로고
    • Modeling protein-protein recognition in solution using the coarse-grained force field SCORPION
    • N. Basdevant et al. Modeling protein-protein recognition in solution using the coarse-grained force field SCORPION J. Chem. Theory. Comput. 9 2013 803 813
    • (2013) J. Chem. Theory. Comput. , vol.9 , pp. 803-813
    • Basdevant, N.1
  • 128
    • 84873694997 scopus 로고    scopus 로고
    • Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations
    • A. Emperador et al. Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations J. Chem. Theory. Comput. 9 2013 1222 1229
    • (2013) J. Chem. Theory. Comput. , vol.9 , pp. 1222-1229
    • Emperador, A.1
  • 129
    • 79956150167 scopus 로고    scopus 로고
    • PyDockCG: New coarse-grained potential for protein-protein docking
    • A. Solernou, and J. Fernandez-Recio pyDockCG: new coarse-grained potential for protein-protein docking J. Phys. Chem. B 115 2011 6032 6039
    • (2011) J. Phys. Chem. B , vol.115 , pp. 6032-6039
    • Solernou, A.1    Fernandez-Recio, J.2
  • 130
    • 84871327327 scopus 로고    scopus 로고
    • ATTRACT-EM: A new method for the computational assembly of large molecular machines using Cryo-EM maps
    • S.J. de Vries, and M. Zacharias ATTRACT-EM: a new method for the computational assembly of large molecular machines using Cryo-EM maps PLoS ONE 7 2012 e49733
    • (2012) PLoS ONE , vol.7 , pp. 49733
    • De Vries, S.J.1    Zacharias, M.2
  • 131
    • 84888288501 scopus 로고    scopus 로고
    • Performance of ZDOCK in CAPRI rounds 20-26
    • T. Vreven et al. Performance of ZDOCK in CAPRI rounds 20-26 Proteins 81 2013 2175 2182
    • (2013) Proteins , vol.81 , pp. 2175-2182
    • Vreven, T.1
  • 132
    • 84888305906 scopus 로고    scopus 로고
    • Flexible docking and refinement with a coarse-grained protein model using ATTRACT
    • S. de Vries, and M. Zacharias Flexible docking and refinement with a coarse-grained protein model using ATTRACT Proteins 81 2013 2167 2174
    • (2013) Proteins , vol.81 , pp. 2167-2174
    • De Vries, S.1    Zacharias, M.2
  • 133
    • 0038187615 scopus 로고    scopus 로고
    • A protein-protein docking benchmark
    • R. Chen et al. A protein-protein docking benchmark Proteins 52 2003 88 91
    • (2003) Proteins , vol.52 , pp. 88-91
    • Chen, R.1
  • 134
    • 21644480883 scopus 로고    scopus 로고
    • Protein-protein docking benchmark 2.0: An update
    • J. Mintseris et al. Protein-protein docking benchmark 2.0: an update Proteins 60 2005 214 216
    • (2005) Proteins , vol.60 , pp. 214-216
    • Mintseris, J.1
  • 135
    • 57349132441 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 3.0
    • H. Hwang et al. Protein-protein docking benchmark version 3.0 Proteins 73 2008 705 709
    • (2008) Proteins , vol.73 , pp. 705-709
    • Hwang, H.1
  • 136
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • H. Hwang et al. Protein-protein docking benchmark version 4.0 Proteins 78 2010 3111 3114
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1
  • 137
    • 79952177781 scopus 로고    scopus 로고
    • A structure-based benchmark for protein-protein binding affinity
    • P. Kastritis et al. A structure-based benchmark for protein-protein binding affinity Protein Sci. 20 2011 482 491
    • (2011) Protein Sci. , vol.20 , pp. 482-491
    • Kastritis, P.1
  • 138
    • 36749060694 scopus 로고    scopus 로고
    • DOCKGROUND system of databases for protein recognition studies: Unbound structures for docking
    • Y. Gao et al. DOCKGROUND system of databases for protein recognition studies: unbound structures for docking Proteins 69 2007 845 851
    • (2007) Proteins , vol.69 , pp. 845-851
    • Gao, Y.1
  • 139
    • 18744382508 scopus 로고    scopus 로고
    • PIBASE: A comprehensive database of structurally defined protein interfaces
    • F.P. Davis, and A. Sali PIBASE: a comprehensive database of structurally defined protein interfaces Bioinformatics 21 2005 1901 1907
    • (2005) Bioinformatics , vol.21 , pp. 1901-1907
    • Davis, F.P.1    Sali, A.2
  • 140
    • 33751415854 scopus 로고    scopus 로고
    • 3D complex: A structural classification of protein complexes
    • E.D. Levy et al. 3D complex: a structural classification of protein complexes PLoS Comput. Biol. 2 2006 e155
    • (2006) PLoS Comput. Biol. , vol.2 , pp. 155
    • Levy, E.D.1
  • 141
    • 33750406198 scopus 로고    scopus 로고
    • DOCKGROUND resource for studying protein-protein interfaces
    • D. Douguet et al. DOCKGROUND resource for studying protein-protein interfaces Bioinformatics 22 2006 2612 2618
    • (2006) Bioinformatics , vol.22 , pp. 2612-2618
    • Douguet, D.1
  • 142
    • 33644876493 scopus 로고    scopus 로고
    • SCOPPI: A structural classification of protein-protein interfaces
    • C. Winter et al. SCOPPI: a structural classification of protein-protein interfaces Nucleic Acids Res. 34 2006 D310 D314
    • (2006) Nucleic Acids Res. , vol.34
    • Winter, C.1
  • 143
    • 24344487344 scopus 로고    scopus 로고
    • Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    • S. Mintz et al. Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions Proteins 61 2005 6 20
    • (2005) Proteins , vol.61 , pp. 6-20
    • Mintz, S.1
  • 144
    • 33846077881 scopus 로고    scopus 로고
    • PROTCOM: Searchable database of protein complexes enhanced with domain-domain structures
    • P.J. Kundrotas, and E. Alexov PROTCOM: searchable database of protein complexes enhanced with domain-domain structures Nucleic Acids Res. 35 2007 D575 D579
    • (2007) Nucleic Acids Res. , vol.35
    • Kundrotas, P.J.1    Alexov, E.2
  • 145
    • 84884761289 scopus 로고    scopus 로고
    • The scoring of poses in protein-protein docking: Current capabilities and future directions
    • I.H. Moal et al. The scoring of poses in protein-protein docking: current capabilities and future directions BMC Bioinformatics 14 2013 286
    • (2013) BMC Bioinformatics , vol.14 , pp. 286
    • Moal, I.H.1
  • 146
    • 36749098356 scopus 로고    scopus 로고
    • The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI
    • K. Wiehe et al. The performance of ZDOCK and ZRANK in rounds 6-11 of CAPRI Proteins 69 2007 719 725
    • (2007) Proteins , vol.69 , pp. 719-725
    • Wiehe, K.1
  • 147
    • 77957963055 scopus 로고    scopus 로고
    • Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19
    • D. Kozakov et al. Achieving reliability and high accuracy in automated protein docking: ClusPro, PIPER, SDU, and stability analysis in CAPRI rounds 13-19 Proteins 78 2010 3124 3130
    • (2010) Proteins , vol.78 , pp. 3124-3130
    • Kozakov, D.1
  • 148
    • 77957956522 scopus 로고    scopus 로고
    • An integrated suite of fast docking algorithms
    • E. Mashiach et al. An integrated suite of fast docking algorithms Proteins 78 2010 3197 3204
    • (2010) Proteins , vol.78 , pp. 3197-3204
    • Mashiach, E.1
  • 149
    • 84888297281 scopus 로고    scopus 로고
    • Defining the limits of homology modeling in information-driven protein docking
    • J.P. Rodrigues et al. Defining the limits of homology modeling in information-driven protein docking Proteins 81 2013 2119 2128
    • (2013) Proteins , vol.81 , pp. 2119-2128
    • Rodrigues, J.P.1
  • 150
    • 84888293785 scopus 로고    scopus 로고
    • A Markov-chain model description of binding funnels to enhance the ranking of docked solutions
    • M. Torchala et al. A Markov-chain model description of binding funnels to enhance the ranking of docked solutions Proteins 81 2013 2143 2149
    • (2013) Proteins , vol.81 , pp. 2143-2149
    • Torchala, M.1
  • 151
    • 84888307602 scopus 로고    scopus 로고
    • Global and local structural similarity in protein-protein complexes: Implications for template-based docking
    • P.J. Kundrotas, and I.A. Vakser Global and local structural similarity in protein-protein complexes: implications for template-based docking Proteins 81 2013 2137 2142
    • (2013) Proteins , vol.81 , pp. 2137-2142
    • Kundrotas, P.J.1    Vakser, I.A.2
  • 152
    • 84888295075 scopus 로고    scopus 로고
    • How good is automated protein docking?
    • D. Kozakov et al. How good is automated protein docking? Proteins 81 2013 2159 2166
    • (2013) Proteins , vol.81 , pp. 2159-2166
    • Kozakov, D.1
  • 153
    • 84888302180 scopus 로고    scopus 로고
    • Expanding the frontiers of protein-protein modeling: From docking and scoring to binding affinity predictions and other challenges
    • C. Pallara et al. Expanding the frontiers of protein-protein modeling: from docking and scoring to binding affinity predictions and other challenges Proteins 81 2013 2192 2200
    • (2013) Proteins , vol.81 , pp. 2192-2200
    • Pallara, C.1
  • 154
    • 84888297609 scopus 로고    scopus 로고
    • Improved flexible refinement of protein docking in CAPRI rounds 22-27
    • Y. Shen Improved flexible refinement of protein docking in CAPRI rounds 22-27 Proteins 81 2013 2129 2136
    • (2013) Proteins , vol.81 , pp. 2129-2136
    • Shen, Y.1
  • 155
    • 84888298806 scopus 로고    scopus 로고
    • Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI
    • S.-Y. Huang et al. Inclusion of the orientational entropic effect and low-resolution experimental information for protein-protein docking in CAPRI Proteins 81 2013 2183 2191
    • (2013) Proteins , vol.81 , pp. 2183-2191
    • Huang, S.-Y.1
  • 156
    • 3242877815 scopus 로고    scopus 로고
    • ClusPro: A fully automated algorithm for protein-protein docking
    • S.R. Comeau et al. ClusPro: a fully automated algorithm for protein-protein docking Nucleic Acids Res. 32 2004 W96 W99
    • (2004) Nucleic Acids Res. , vol.32
    • Comeau, S.R.1
  • 157
    • 77955391393 scopus 로고    scopus 로고
    • The HADDOCK web server for data-driven biomolecular docking
    • S.J. de Vries et al. The HADDOCK web server for data-driven biomolecular docking Nat. Protoc. 5 2010 883 897
    • (2010) Nat. Protoc. , vol.5 , pp. 883-897
    • De Vries, S.J.1
  • 158
    • 48449105393 scopus 로고    scopus 로고
    • The RosettaDock server for local protein-protein docking
    • S. Lyskov, and J.J. Gray The RosettaDock server for local protein-protein docking Nucleic Acids Res. 36 2008 W233 W238
    • (2008) Nucleic Acids Res. , vol.36
    • Lyskov, S.1    Gray, J.J.2
  • 159
    • 33747840389 scopus 로고    scopus 로고
    • GRAMM-X public web server for protein-protein docking
    • A. Tovchigrechko, and I.A. Vakser GRAMM-X public web server for protein-protein docking Nucleic Acids Res. 34 2006 W310 W314
    • (2006) Nucleic Acids Res. , vol.34
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 160
    • 42649122289 scopus 로고    scopus 로고
    • 3D-Garden: A system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm
    • V.I. Lesk, and M.J. Sternberg 3D-Garden: a system for modelling protein-protein complexes based on conformational refinement of ensembles generated with the marching cubes algorithm Bioinformatics 24 2008 1137 1144
    • (2008) Bioinformatics , vol.24 , pp. 1137-1144
    • Lesk, V.I.1    Sternberg, M.J.2
  • 161
    • 77954267296 scopus 로고    scopus 로고
    • FiberDock: A web server for flexible induced-fit backbone refinement in molecular docking
    • E. Mashiach et al. FiberDock: a web server for flexible induced-fit backbone refinement in molecular docking Nucleic Acids Res. 38 2010 W457 W461
    • (2010) Nucleic Acids Res. , vol.38
    • Mashiach, E.1
  • 162
    • 77954275738 scopus 로고    scopus 로고
    • HexServer: An FFT-based protein docking server powered by graphics processors
    • G. Macindoe et al. HexServer: an FFT-based protein docking server powered by graphics processors Nucleic Acids Res. 38 2010 W445 W449
    • (2010) Nucleic Acids Res. , vol.38
    • Macindoe, G.1
  • 163
    • 84875151263 scopus 로고    scopus 로고
    • SwarmDock: A server for flexible protein-protein docking
    • M. Torchala et al. SwarmDock: a server for flexible protein-protein docking Bioinformatics 29 2013 807 809
    • (2013) Bioinformatics , vol.29 , pp. 807-809
    • Torchala, M.1
  • 164
    • 84897980054 scopus 로고    scopus 로고
    • ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers
    • B.G. Pierce et al. ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers Bioinformatics 2014 http://dx.doi.org/10.1093/bioinformatics/btu097
    • (2014) Bioinformatics
    • Pierce, B.G.1
  • 165
    • 84879916282 scopus 로고    scopus 로고
    • PyDockWEB: A web server for rigid-body protein-protein docking using electrostatics and desolvation scoring
    • B. Jimenez-Garcia et al. pyDockWEB: a web server for rigid-body protein-protein docking using electrostatics and desolvation scoring Bioinformatics 29 2013 1698 1699
    • (2013) Bioinformatics , vol.29 , pp. 1698-1699
    • Jimenez-Garcia, B.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.