메뉴 건너뛰기




Volumn 108, Issue 3, 2015, Pages 462-465

A web interface for easy flexible protein-protein docking with ATTRACT

Author keywords

[No Author keywords available]

Indexed keywords

CCL2 PROTEIN, MOUSE; MONOCYTE CHEMOTACTIC PROTEIN 1; PROTEIN BINDING; VIRUS PROTEIN;

EID: 84947201463     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2014.12.015     Document Type: Article
Times cited : (90)

References (26)
  • 1
    • 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
  • 2
    • 3242877815 scopus 로고    scopus 로고
    • CLUSPRO: A fully automated algorithm for protein-protein docking
    • S.R. Comeau, and D.W. Gatchell C.J. Camacho CLUSPRO: a fully automated algorithm for protein-protein docking Nucleic Acids Res. 32 2004 W96 W99
    • (2004) Nucleic Acids Res. , vol.32 , pp. W96-W99
    • Comeau, S.R.1    Gatchell, D.W.2    Camacho, C.J.3
  • 3
    • 21644476468 scopus 로고    scopus 로고
    • PATCHDOCK and SYMMDOCK: Servers for rigid and symmetric docking
    • D. Schneidman-Duhovny, and Y. Inbar H.J. Wolfson PATCHDOCK and SYMMDOCK: servers for rigid and symmetric docking Nucleic Acids Res. 33 2005 W363 W367
    • (2005) Nucleic Acids Res. , vol.33 , pp. W363-W367
    • Schneidman-Duhovny, D.1    Inbar, Y.2    Wolfson, H.J.3
  • 4
    • 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 , pp. W310-W314
    • Tovchigrechko, A.1    Vakser, I.A.2
  • 5
    • 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 , pp. W233-W238
    • Lyskov, S.1    Gray, J.J.2
  • 6
    • 77955391393 scopus 로고    scopus 로고
    • The HADDOCK web server for data-driven biomolecular docking
    • S.J. de Vries, M. van Dijk, and A.M. Bonvin 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    Van Dijk, M.2    Bonvin, A.M.3
  • 7
    • 77954275738 scopus 로고    scopus 로고
    • HEXSERVER: An FFT-based protein docking server powered by graphics processors
    • G. Macindoe, and L. Mavridis D.W. Ritchie HEXSERVER: an FFT-based protein docking server powered by graphics processors Nucleic Acids Res. 38 2010 W445 W449
    • (2010) Nucleic Acids Res. , vol.38 , pp. W445-W449
    • Macindoe, G.1    Mavridis, L.2    Ritchie, D.W.3
  • 8
    • 84875151263 scopus 로고    scopus 로고
    • SWARMDOCK: A server for flexible protein-protein docking
    • M. Torchala, and I.H. Moal P.A. Bates SWARMDOCK: a server for flexible protein-protein docking Bioinformatics 29 2013 807 809
    • (2013) Bioinformatics , vol.29 , pp. 807-809
    • Torchala, M.1    Moal, I.H.2    Bates, P.A.3
  • 9
    • 84897980054 scopus 로고    scopus 로고
    • ZDOCK server: Interactive docking prediction of protein-protein complexes and symmetric multimers
    • B.G. Pierce, and K. Wiehe Z. Weng ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers Bioinformatics 30 2014 1771 1773
    • (2014) Bioinformatics , vol.30 , pp. 1771-1773
    • Pierce, B.G.1    Wiehe, K.2    Weng, Z.3
  • 10
    • 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
  • 11
    • 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
  • 12
    • 36749035257 scopus 로고    scopus 로고
    • Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
    • A. May, and M. Zacharias Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility Proteins. 69 2007 774 780
    • (2007) Proteins. , vol.69 , pp. 774-780
    • May, A.1    Zacharias, M.2
  • 13
    • 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
  • 14
    • 77957958670 scopus 로고    scopus 로고
    • Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT
    • S. Fiorucci, and M. Zacharias Binding site prediction and improved scoring during flexible protein-protein docking with ATTRACT Proteins. 78 2010 3131 3139
    • (2010) Proteins. , vol.78 , pp. 3131-3139
    • Fiorucci, S.1    Zacharias, M.2
  • 15
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    • A. May, and M. Zacharias Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking Proteins. 70 2008 794 809
    • (2008) Proteins. , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 16
    • 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. e49733
    • De Vries, S.J.1    Zacharias, M.2
  • 17
    • 84865984820 scopus 로고    scopus 로고
    • Protein-DNA docking with a coarse-grained force field
    • P. Setny, R.P. Bahadur, and M. Zacharias Protein-DNA docking with a coarse-grained force field BMC Bioinformatics 13 2012 228
    • (2012) BMC Bioinformatics , vol.13 , pp. 228
    • Setny, P.1    Bahadur, R.P.2    Zacharias, M.3
  • 18
    • 82255164407 scopus 로고    scopus 로고
    • A coarse-grained force field for protein-RNA docking
    • P. Setny, and M. Zacharias A coarse-grained force field for protein-RNA docking Nucleic Acids Res. 39 2011 9118 9129
    • (2011) Nucleic Acids Res. , vol.39 , pp. 9118-9129
    • Setny, P.1    Zacharias, M.2
  • 19
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for global protein deformability during protein-protein and protein-ligand docking
    • A. May, and M. Zacharias Accounting for global protein deformability during protein-protein and protein-ligand docking Biochim. Biophys. Acta 1754 2005 225 231
    • (2005) Biochim. Biophys. Acta , vol.1754 , pp. 225-231
    • May, A.1    Zacharias, M.2
  • 20
    • 84937575796 scopus 로고    scopus 로고
    • IATTRACT: Simultaneous global and local interface optimization for protein-protein docking refinement
    • Published online November 17, 2014
    • C.E. Schindler, S.J. De Vries, and M. Zacharias iATTRACT: simultaneous global and local interface optimization for protein-protein docking refinement Proteins 2014 10.1002/prot.24728 Published online November 17, 2014
    • (2014) Proteins
    • Schindler, C.E.1    De Vries, S.J.2    Zacharias, M.3
  • 21
    • 79953040045 scopus 로고    scopus 로고
    • CPORT: A consensus interface predictor and its performance in prediction-driven docking with HADDOCK
    • S.J. de Vries, and A.M. Bonvin CPORT: a consensus interface predictor and its performance in prediction-driven docking with HADDOCK PLoS ONE 6 2011 e17695
    • (2011) PLoS ONE , vol.6 , pp. e17695
    • De Vries, S.J.1    Bonvin, A.M.2
  • 22
    • 0036218112 scopus 로고    scopus 로고
    • Critical role for a high-affinity chemokine-binding protein in γ-herpesvirus-induced lethal meningitis
    • V. van Berkel, and B. Levine H.W. Virgin 4th Critical role for a high-affinity chemokine-binding protein in γ-herpesvirus-induced lethal meningitis J. Clin. Invest. 109 2002 905 914
    • (2002) J. Clin. Invest. , vol.109 , pp. 905-914
    • Van Berkel, V.1    Levine, B.2    Virgin, H.W.3
  • 23
    • 0030738667 scopus 로고    scopus 로고
    • Complete sequence and genomic analysis of murine γ-herpesvirus 68
    • H.W. Virgin 4th, and P. Latreille S.H. Speck Complete sequence and genomic analysis of murine γ-herpesvirus 68 J. Virol. 71 1997 5894 5904
    • (1997) J. Virol. , vol.71 , pp. 5894-5904
    • Virgin, H.W.1    Latreille, P.2    Speck, S.H.3
  • 24
    • 18744401050 scopus 로고    scopus 로고
    • Structural basis of chemokine sequestration by a herpesvirus decoy receptor
    • J.M. Alexander, and C.A. Nelson D.H. Fremont Structural basis of chemokine sequestration by a herpesvirus decoy receptor Cell 111 2002 343 356
    • (2002) Cell , vol.111 , pp. 343-356
    • Alexander, J.M.1    Nelson, C.A.2    Fremont, D.H.3
  • 25
    • 0031026207 scopus 로고    scopus 로고
    • The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions
    • J. Lubkowski, and G. Bujacz A. Wlodawer The structure of MCP-1 in two crystal forms provides a rare example of variable quaternary interactions Nat. Struct. Biol. 4 1997 64 69
    • (1997) Nat. Struct. Biol. , vol.4 , pp. 64-69
    • Lubkowski, J.1    Bujacz, G.2    Wlodawer, A.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.