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Volumn 55, Issue 7, 2015, Pages 1495-1507

ProPairs: A Data Set for Protein-Protein Docking

Author keywords

[No Author keywords available]

Indexed keywords

DOCKING;

EID: 84938057090     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00082     Document Type: Article
Times cited : (13)

References (51)
  • 2
    • 0036088133 scopus 로고    scopus 로고
    • Dip, the Database of Interacting Proteins: A Research Tool for Studying Cellular Networks of Protein Interactions
    • Xenarios, I.; Salwinski, L.; Duan, X. J.; Higney, P.; Kim, S.-M.; Eisenberg, D. Dip, the Database of Interacting Proteins: A Research Tool for Studying Cellular Networks of Protein Interactions Nucleic Acids Res. 2002, 30, 303-305
    • (2002) Nucleic Acids Res. , vol.30 , pp. 303-305
    • Xenarios, I.1    Salwinski, L.2    Duan, X.J.3    Higney, P.4    Kim, S.-M.5    Eisenberg, D.6
  • 6
    • 33644550021 scopus 로고    scopus 로고
    • Structural Systems Biology: Modelling Protein Interactions
    • Aloy, P.; Russell, R. B. Structural Systems Biology: Modelling Protein Interactions Nat. Rev. Mol. Cell Biol. 2006, 7, 188-197
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 7
    • 33749234216 scopus 로고    scopus 로고
    • Drugs, Their Targets and the Nature and Number of Drug Targets
    • Imming, P.; Sinning, C.; Meyer, A. Drugs, Their Targets and the Nature and Number of Drug Targets Nat. Rev. Drug Discovery 2006, 5, 821-834
    • (2006) Nat. Rev. Drug Discovery , vol.5 , pp. 821-834
    • Imming, P.1    Sinning, C.2    Meyer, A.3
  • 8
    • 79960990847 scopus 로고    scopus 로고
    • Chemical and Structural Lessons from Recent Successes in Protein-Protein Interaction Inhibition (2p2i)
    • Morelli, X.; Bourgeas, R.; Roche, P. Chemical and Structural Lessons from Recent Successes in Protein-Protein Interaction Inhibition (2p2i) Curr. Opin. Chem. Biol. 2011, 15, 475-481
    • (2011) Curr. Opin. Chem. Biol. , vol.15 , pp. 475-481
    • Morelli, X.1    Bourgeas, R.2    Roche, P.3
  • 9
    • 37249004920 scopus 로고    scopus 로고
    • Reaching for High-Hanging Fruit in Drug Discovery at Protein-Protein Interfaces
    • Wells, J. A.; McClendon, C. L. Reaching for High-Hanging Fruit in Drug Discovery at Protein-Protein Interfaces Nature 2007, 450, 1001-1009
    • (2007) Nature , vol.450 , pp. 1001-1009
    • Wells, J.A.1    McClendon, C.L.2
  • 10
    • 84866309070 scopus 로고    scopus 로고
    • Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application
    • Metz, A.; Ciglia, E.; Gohlke, H. Modulating Protein-Protein Interactions: From Structural Determinants of Binding to Druggability Prediction to Application Curr. Pharm. Des. 2012, 18, 4630-4647
    • (2012) Curr. Pharm. Des. , vol.18 , pp. 4630-4647
    • Metz, A.1    Ciglia, E.2    Gohlke, H.3
  • 11
    • 76149109071 scopus 로고    scopus 로고
    • Targeting Protein-Protein Interactions for Therapeutic Intervention: A Challenge for the Future
    • Zinzalla, G.; Thurston, D. E. Targeting Protein-Protein Interactions for Therapeutic Intervention: A Challenge for the Future Future Med. Chem. 2009, 1, 65-93
    • (2009) Future Med. Chem. , vol.1 , pp. 65-93
    • Zinzalla, G.1    Thurston, D.E.2
  • 14
    • 13844255392 scopus 로고    scopus 로고
    • Protein Complexes: Structure Prediction Challenges for the 21st Century
    • Aloy, P.; Pichaud, M.; Russell, R. B. Protein Complexes: Structure Prediction Challenges for the 21st Century Curr. Opin. Struct. Biol. 2005, 15, 15-22
    • (2005) Curr. Opin. Struct. Biol. , vol.15 , pp. 15-22
    • Aloy, P.1    Pichaud, M.2    Russell, R.B.3
  • 15
    • 41949111630 scopus 로고    scopus 로고
    • Recent Progress and Future Directions in Protein-Protein Docking
    • Ritchie, D. W. Recent Progress and Future Directions in Protein-Protein Docking Curr. Protein Pept. Sci. 2008, 9, 1-15
    • (2008) Curr. Protein Pept. Sci. , vol.9 , pp. 1-15
    • Ritchie, D.W.1
  • 16
    • 78149422216 scopus 로고    scopus 로고
    • Protein-Protein Docking Tested in Blind Predictions: The Capri Experiment
    • Janin, J. Protein-Protein Docking Tested in Blind Predictions: The Capri Experiment Mol. BioSyst. 2010, 6, 2351-2362
    • (2010) Mol. BioSyst. , vol.6 , pp. 2351-2362
    • Janin, J.1
  • 17
    • 79958064379 scopus 로고    scopus 로고
    • Challenges for the Prediction of Macromolecular Interactions
    • Wass, M. N.; David, A.; Sternberg, M. J. Challenges for the Prediction of Macromolecular Interactions Curr. Opin. Struct. Biol. 2011, 21, 382-390
    • (2011) Curr. Opin. Struct. Biol. , vol.21 , pp. 382-390
    • Wass, M.N.1    David, A.2    Sternberg, M.J.3
  • 20
    • 84908263546 scopus 로고    scopus 로고
    • Protein-Protein Docking: From Interaction to Interactome
    • Vakser, I. A. Protein-Protein Docking: From Interaction to Interactome Biophys. J. 2014, 107, 1785-1793
    • (2014) Biophys. J. , vol.107 , pp. 1785-1793
    • Vakser, I.A.1
  • 21
    • 84878552481 scopus 로고    scopus 로고
    • Low-Resolution Structural Modeling of Protein Interactome
    • Vakser, I. A. Low-Resolution Structural Modeling of Protein Interactome Curr. Opin. Struct. Biol. 2013, 23, 198-205
    • (2013) Curr. Opin. Struct. Biol. , vol.23 , pp. 198-205
    • Vakser, I.A.1
  • 22
    • 0018165127 scopus 로고
    • Computer Analysis of Protein-Protein Interaction
    • Wodak, S. J.; Janin, J. Computer Analysis of Protein-Protein Interaction J. Mol. Biol. 1978, 124, 323-342
    • (1978) J. Mol. Biol. , vol.124 , pp. 323-342
    • Wodak, S.J.1    Janin, J.2
  • 23
    • 36549102274 scopus 로고
    • Brownian Dynamics Simulation of Diffusion-Influenced Bimolecular Reactions
    • Northrup, S. H.; Allison, S. A.; McCammon, J. A. Brownian Dynamics Simulation of Diffusion-Influenced Bimolecular Reactions J. Chem. Phys. 1984, 80, 1517-1524
    • (1984) J. Chem. Phys. , vol.80 , pp. 1517-1524
    • Northrup, S.H.1    Allison, S.A.2    McCammon, J.A.3
  • 24
    • 0031041540 scopus 로고    scopus 로고
    • Computational Simulation and Analysis of Dynamic Association between Plastocyanin and Cytochrome F. Consequences for the Electron-Transfer Reaction
    • Ullmann, G. M.; Knapp, E. W.; Kostic, N. M. Computational Simulation and Analysis of Dynamic Association between Plastocyanin and Cytochrome F. Consequences for the Electron-Transfer Reaction J. Am. Chem. Soc. 1997, 119, 42-52
    • (1997) J. Am. Chem. Soc. , vol.119 , pp. 42-52
    • Ullmann, G.M.1    Knapp, E.W.2    Kostic, N.M.3
  • 25
    • 0037442962 scopus 로고    scopus 로고
    • Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information
    • Dominguez, C.; Boelens, R.; Bonvin, A. M. Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information J. Am. Chem. Soc. 2003, 125, 1731-1737
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 26
    • 84855256224 scopus 로고    scopus 로고
    • Scoring Optimisation of Unbound Protein-Protein Docking Including Protein Binding Site Predictions
    • Schneider, S.; Zacharias, M. Scoring Optimisation of Unbound Protein-Protein Docking Including Protein Binding Site Predictions J. Mol. Recognit. 2012, 25, 15-23
    • (2012) J. Mol. Recognit. , vol.25 , pp. 15-23
    • Schneider, S.1    Zacharias, M.2
  • 30
  • 31
    • 36749060694 scopus 로고    scopus 로고
    • Dockground System of Databases for Protein Recognition Studies: Unbound Structures for Docking
    • Gao, Y.; Douguet, D.; Tovchigrechko, A.; Vakser, I. A. Dockground System of Databases for Protein Recognition Studies: Unbound Structures for Docking Proteins: Struct., Funct., Bioinf. 2007, 69, 845-851
    • (2007) Proteins: Struct., Funct., Bioinf. , vol.69 , pp. 845-851
    • Gao, Y.1    Douguet, D.2    Tovchigrechko, A.3    Vakser, I.A.4
  • 32
    • 84898032675 scopus 로고    scopus 로고
    • Database of Protein Complexes with Multivalent Binding Ability: Bival-Bind
    • Meyer, T.; Knapp, E. W. Database of Protein Complexes with Multivalent Binding Ability: Bival-Bind Proteins: Struct., Funct., Bioinf. 2014, 82, 744-751
    • (2014) Proteins: Struct., Funct., Bioinf. , vol.82 , pp. 744-751
    • Meyer, T.1    Knapp, E.W.2
  • 33
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of Blind Predictions of Protein-Protein Interactions: Current Status of Docking Methods
    • Méndez, R.; Leplae, R.; De Maria, L.; Wodak, S. J. Assessment of Blind Predictions of Protein-Protein Interactions: Current Status of Docking Methods Proteins: Struct., Funct., Bioinf. 2003, 52, 51-67
    • (2003) Proteins: Struct., Funct., Bioinf. , vol.52 , pp. 51-67
    • Méndez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 34
    • 49249118038 scopus 로고    scopus 로고
    • A Protein-DNA Docking Benchmark
    • van Dijk, M.; Bonvin, A. M. A Protein-DNA Docking Benchmark Nucleic Acids Res. 2008, 36, e88-e88
    • (2008) Nucleic Acids Res. , vol.36 , pp. e88-e88
    • Van Dijk, M.1    Bonvin, A.M.2
  • 36
    • 0019887799 scopus 로고
    • Identification of Common Molecular Subsequences
    • Smith, T. F.; Waterman, M. S. Identification of Common Molecular Subsequences J. Mol. Biol. 1981, 147, 195-197
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 37
    • 79960884702 scopus 로고    scopus 로고
    • Comprehensive, Atomic-Level Characterization of Structurally Characterized Protein-Protein Interactions: The Piccolo Database
    • Bickerton, G. R.; Higueruelo, A. P.; Blundell, T. L. Comprehensive, Atomic-Level Characterization of Structurally Characterized Protein-Protein Interactions: The Piccolo Database BMC Bioinf. 2011, 12, 313-313
    • (2011) BMC Bioinf. , vol.12 , pp. 313-313
    • Bickerton, G.R.1    Higueruelo, A.P.2    Blundell, T.L.3
  • 39
    • 44849127103 scopus 로고    scopus 로고
    • Alignment of Non-Covalent Interactions at Protein-Protein Interfaces
    • Zhu, H.; Sommer, I.; Lengauer, T.; Domingues, F. S. Alignment of Non-Covalent Interactions at Protein-Protein Interfaces PLoS One 2008, 3, e1926
    • (2008) PLoS One , vol.3 , pp. 1926
    • Zhu, H.1    Sommer, I.2    Lengauer, T.3    Domingues, F.S.4
  • 40
    • 23144456254 scopus 로고    scopus 로고
    • Siteengines: Recognition and Comparison of Binding Sites and Protein-Protein Interfaces
    • Shulman-Peleg, A.; Nussinov, R.; Wolfson, H. J. Siteengines: Recognition and Comparison of Binding Sites and Protein-Protein Interfaces Nucleic Acids Res. 2005, 33, W337-W341
    • (2005) Nucleic Acids Res. , vol.33 , pp. W337-W341
    • Shulman-Peleg, A.1    Nussinov, R.2    Wolfson, H.J.3
  • 41
    • 53749101674 scopus 로고    scopus 로고
    • Optimal Contact Map Alignment of Protein-Protein Interfaces
    • Pulim, V.; Berger, B.; Bienkowska, J. Optimal Contact Map Alignment of Protein-Protein Interfaces Bioinformatics 2008, 24, 2324-2328
    • (2008) Bioinformatics , vol.24 , pp. 2324-2328
    • Pulim, V.1    Berger, B.2    Bienkowska, J.3
  • 42
    • 77956502131 scopus 로고    scopus 로고
    • Ialign: A Method for the Structural Comparison of Protein-Protein Interfaces
    • Gao, M.; Skolnick, J. Ialign: A Method for the Structural Comparison of Protein-Protein Interfaces Bioinformatics 2010, 26, 2259-2265
    • (2010) Bioinformatics , vol.26 , pp. 2259-2265
    • Gao, M.1    Skolnick, J.2
  • 43
    • 0030602896 scopus 로고    scopus 로고
    • A Dataset of Protein-Protein Interfaces Generated with a Sequence-Order-Independent Comparison Technique
    • Tsai, C.-J.; Lin, S. L.; Wolfson, H. J.; Nussinov, R. A Dataset of Protein-Protein Interfaces Generated with a Sequence-Order-Independent Comparison Technique J. Mol. Biol. 1996, 260, 604-620
    • (1996) J. Mol. Biol. , vol.260 , pp. 604-620
    • Tsai, C.-J.1    Lin, S.L.2    Wolfson, H.J.3    Nussinov, R.4
  • 44
    • 0028961335 scopus 로고
    • Scop: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures
    • Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. Scop: A Structural Classification of Proteins Database for the Investigation of Sequences and Structures J. Mol. Biol. 1995, 247, 536-540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 45
    • 84891811692 scopus 로고    scopus 로고
    • Scope: Structural Classification of Proteins - Extended, Integrating Scop and Astral Data and Classification of New Structures
    • Fox, N. K.; Brenner, S. E.; Chandonia, J.-M. Scope: Structural Classification of Proteins-Extended, Integrating Scop and Astral Data and Classification of New Structures Nucleic Acids Res. 2014, 42, D304-D309
    • (2014) Nucleic Acids Res. , vol.42 , pp. D304-D309
    • Fox, N.K.1    Brenner, S.E.2    Chandonia, J.-M.3
  • 47
    • 0028566271 scopus 로고
    • The Subunit Interfaces of Oligomeric Enzymes Are Conserved to a Similar Extent to the Overall Protein Sequences
    • Grishin, N. V.; Phillips, M. A. The Subunit Interfaces of Oligomeric Enzymes Are Conserved to a Similar Extent to the Overall Protein Sequences Protein Sci. 1994, 3, 2455-2458
    • (1994) Protein Sci. , vol.3 , pp. 2455-2458
    • Grishin, N.V.1    Phillips, M.A.2
  • 48
    • 0035178383 scopus 로고    scopus 로고
    • Protein-Protein Interfaces: Analysis of Amino Acid Conservation in Homodimers
    • Valdar, W. S.; Thornton, J. M. Protein-Protein Interfaces: Analysis of Amino Acid Conservation in Homodimers Proteins: Struct., Funct., Bioinf. 2001, 42, 108-124
    • (2001) Proteins: Struct., Funct., Bioinf. , vol.42 , pp. 108-124
    • Valdar, W.S.1    Thornton, J.M.2
  • 49
    • 0037229456 scopus 로고    scopus 로고
    • Analysing Six Types of Protein-Protein Interfaces
    • Ofran, Y.; Rost, B. Analysing Six Types of Protein-Protein Interfaces J. Mol. Biol. 2003, 325, 377-387
    • (2003) J. Mol. Biol. , vol.325 , pp. 377-387
    • Ofran, Y.1    Rost, B.2
  • 50
    • 0346733329 scopus 로고    scopus 로고
    • Are Protein-Protein Interfaces More Conserved in Sequence Than the Rest of the Protein Surface?
    • Caffrey, D. R.; Somaroo, S.; Hughes, J. D.; Mintseris, J.; Huang, E. S. Are Protein-Protein Interfaces More Conserved in Sequence Than the Rest of the Protein Surface? Protein Sci. 2004, 13, 190-202
    • (2004) Protein Sci. , vol.13 , pp. 190-202
    • Caffrey, D.R.1    Somaroo, S.2    Hughes, J.D.3    Mintseris, J.4    Huang, E.S.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.