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Volumn 22, Issue 9, 2014, Pages 1356-1362

Assessing the applicability of template-based protein docking in the twilight zone

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN; PROTEIN BINDING;

EID: 84930063678     PISSN: 09692126     EISSN: 18784186     Source Type: Journal    
DOI: 10.1016/j.str.2014.07.009     Document Type: Article
Times cited : (28)

References (36)
  • 1
    • 33644550021 scopus 로고    scopus 로고
    • Structural systems biology: Modelling protein interactions
    • P. Aloy, and R.B. Russell Structural systems biology: modelling protein interactions Nat. Rev. Mol. Cell Biol. 7 2006 188 197
    • (2006) Nat. Rev. Mol. Cell Biol. , vol.7 , pp. 188-197
    • Aloy, P.1    Russell, R.B.2
  • 2
    • 0042386609 scopus 로고    scopus 로고
    • The relationship between sequence and interaction divergence in proteins
    • P. Aloy, H. Ceulemans, A. Stark, and R.B. Russell The relationship between sequence and interaction divergence in proteins J. Mol. Biol. 332 2003 989 998
    • (2003) J. Mol. Biol. , vol.332 , pp. 989-998
    • Aloy, P.1    Ceulemans, H.2    Stark, A.3    Russell, R.B.4
  • 3
    • 84857780876 scopus 로고    scopus 로고
    • Evidence for network evolution in an Arabidopsis interactome map
    • Arabidopsis Interactome Mapping Consortium
    • Arabidopsis Interactome Mapping Consortium Evidence for network evolution in an Arabidopsis interactome map Science 333 2011 601 607
    • (2011) Science , vol.333 , pp. 601-607
  • 5
    • 0032568596 scopus 로고    scopus 로고
    • Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships
    • S.E. Brenner, C. Chothia, and T.J. Hubbard Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships Proc. Natl. Acad. Sci. USA 95 1998 6073 6078
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 6073-6078
    • Brenner, S.E.1    Chothia, C.2    Hubbard, T.J.3
  • 6
    • 36448963759 scopus 로고    scopus 로고
    • Host pathogen protein interactions predicted by comparative modeling
    • F.P. Davis, D.T. Barkan, N. Eswar, J.H. McKerrow, and A. Sali Host pathogen protein interactions predicted by comparative modeling Protein Sci. 16 2007 2585 2596
    • (2007) Protein Sci. , vol.16 , pp. 2585-2596
    • Davis, F.P.1    Barkan, D.T.2    Eswar, N.3    McKerrow, J.H.4    Sali, A.5
  • 7
  • 8
    • 84878242555 scopus 로고    scopus 로고
    • Structural systems pharmacology: The role of 3D structures in next-generation drug development
    • M. Duran-Frigola, R. Mosca, and P. Aloy Structural systems pharmacology: the role of 3D structures in next-generation drug development Chem. Biol. 20 2013 674 684
    • (2013) Chem. Biol. , vol.20 , pp. 674-684
    • Duran-Frigola, M.1    Mosca, R.2    Aloy, P.3
  • 9
    • 36749058849 scopus 로고    scopus 로고
    • Docking without docking: ISEARCH - Prediction of interactions using known interfaces
    • S. Günther, P. May, A. Hoppe, C. Frömmel, and R. Preissner Docking without docking: ISEARCH - prediction of interactions using known interfaces Proteins 69 2007 839 844
    • (2007) Proteins , vol.69 , pp. 839-844
    • Günther, S.1    May, P.2    Hoppe, A.3    Frömmel, C.4    Preissner, R.5
  • 10
    • 77957944014 scopus 로고    scopus 로고
    • Protein-protein docking benchmark version 4.0
    • H. Hwang, T. Vreven, J. Janin, and Z. Weng Protein-protein docking benchmark version 4.0 Proteins 78 2010 3111 3114
    • (2010) Proteins , vol.78 , pp. 3111-3114
    • Hwang, H.1    Vreven, T.2    Janin, J.3    Weng, Z.4
  • 11
    • 84884483881 scopus 로고    scopus 로고
    • Advances in integrative modeling of biomolecular complexes
    • E. Karaca, and A.M. Bonvin Advances in integrative modeling of biomolecular complexes Methods 59 2013 372 381
    • (2013) Methods , vol.59 , pp. 372-381
    • Karaca, E.1    Bonvin, A.M.2
  • 13
    • 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
  • 15
    • 84862233055 scopus 로고    scopus 로고
    • Templates are available to model nearly all complexes of structurally characterized proteins
    • P.J. Kundrotas, Z. Zhu, J. Janin, and I.A. Vakser Templates are available to model nearly all complexes of structurally characterized proteins Proc. Natl. Acad. Sci. USA 109 2012 9438 9441
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 9438-9441
    • Kundrotas, P.J.1    Zhu, Z.2    Janin, J.3    Vakser, I.A.4
  • 16
  • 17
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • R. Méndez, R. Leplae, L. De Maria, and S.J. Wodak 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
    • Méndez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 18
    • 70049112107 scopus 로고    scopus 로고
    • Pushing structural information into the yeast interactome by high-throughput protein docking experiments
    • R. Mosca, C. Pons, J. Fernández-Recio, and P. Aloy Pushing structural information into the yeast interactome by high-throughput protein docking experiments PLoS Comput. Biol. 5 2009 e1000490
    • (2009) PLoS Comput. Biol. , vol.5 , pp. 1000490
    • Mosca, R.1    Pons, C.2    Fernández-Recio, J.3    Aloy, P.4
  • 19
    • 84871967106 scopus 로고    scopus 로고
    • Interactome3D: Adding structural details to protein networks
    • R. Mosca, A. Céol, and P. Aloy Interactome3D: adding structural details to protein networks Nat. Methods 10 2013 47 53
    • (2013) Nat. Methods , vol.10 , pp. 47-53
    • Mosca, R.1    Céol, A.2    Aloy, P.3
  • 21
    • 67649869968 scopus 로고    scopus 로고
    • MM-align: A quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming
    • S. Mukherjee, and Y. Zhang MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming Nucleic Acids Res. 37 2009 e83
    • (2009) Nucleic Acids Res. , vol.37 , pp. 83
    • Mukherjee, S.1    Zhang, Y.2
  • 22
    • 44649187518 scopus 로고    scopus 로고
    • Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits
    • R.A. Pache, and P. Aloy Incorporating high-throughput proteomics experiments into structural biology pipelines: identification of the low-hanging fruits Proteomics 8 2008 1959 1964
    • (2008) Proteomics , vol.8 , pp. 1959-1964
    • Pache, R.A.1    Aloy, P.2
  • 23
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • W.R. Pearson, and D.J. Lipman Improved tools for biological sequence comparison Proc. Natl. Acad. Sci. USA 85 1988 2444 2448
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 26
    • 77957959671 scopus 로고    scopus 로고
    • Docking by structural similarity at protein-protein interfaces
    • R. Sinha, P.J. Kundrotas, and I.A. Vakser Docking by structural similarity at protein-protein interfaces Proteins 78 2010 3235 3241
    • (2010) Proteins , vol.78 , pp. 3235-3241
    • Sinha, R.1    Kundrotas, P.J.2    Vakser, I.A.3
  • 27
    • 84856940901 scopus 로고    scopus 로고
    • Protein docking by the interface structure similarity: How much structure is needed?
    • R. Sinha, P.J. Kundrotas, and I.A. Vakser Protein docking by the interface structure similarity: how much structure is needed? PLoS ONE 7 2012 e31349
    • (2012) PLoS ONE , vol.7 , pp. 31349
    • Sinha, R.1    Kundrotas, P.J.2    Vakser, I.A.3
  • 29
    • 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
  • 30
    • 79956188706 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: Unifying evolution and structure at protein interfaces
    • N. Tuncbag, A. Gursoy, and O. Keskin Prediction of protein-protein interactions: unifying evolution and structure at protein interfaces Phys. Biol. 8 2011 035006
    • (2011) Phys. Biol. , vol.8 , pp. 035006
    • Tuncbag, N.1    Gursoy, A.2    Keskin, O.3
  • 31
    • 84857790849 scopus 로고    scopus 로고
    • Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement
    • N. Tuncbag, O. Keskin, R. Nussinov, and A. Gursoy Fast and accurate modeling of protein-protein interactions by combining template-interface-based docking with flexible refinement Proteins 80 2012 1239 1249
    • (2012) Proteins , vol.80 , pp. 1239-1249
    • Tuncbag, N.1    Keskin, O.2    Nussinov, R.3    Gursoy, A.4
  • 32
    • 84857788445 scopus 로고    scopus 로고
    • Large-scale mapping of human protein interactome using structural complexes
    • M. Tyagi, K. Hashimoto, B.A. Shoemaker, S. Wuchty, and A.R. Panchenko Large-scale mapping of human protein interactome using structural complexes EMBO Rep. 13 2012 266 271
    • (2012) EMBO Rep. , vol.13 , pp. 266-271
    • Tyagi, M.1    Hashimoto, K.2    Shoemaker, B.A.3    Wuchty, S.4    Panchenko, A.R.5
  • 34
    • 10344232638 scopus 로고    scopus 로고
    • Scoring function for automated assessment of protein structure template quality
    • Y. Zhang, and J. Skolnick Scoring function for automated assessment of protein structure template quality Proteins 57 2004 702 710
    • (2004) Proteins , vol.57 , pp. 702-710
    • Zhang, Y.1    Skolnick, J.2
  • 35
    • 17644392830 scopus 로고    scopus 로고
    • TM-align: A protein structure alignment algorithm based on the TM-score
    • Y. Zhang, and J. Skolnick TM-align: a protein structure alignment algorithm based on the TM-score Nucleic Acids Res. 33 2005 2302 2309
    • (2005) Nucleic Acids Res. , vol.33 , pp. 2302-2309
    • Zhang, Y.1    Skolnick, J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.