메뉴 건너뛰기




Volumn 69, Issue 4, 2007, Pages 774-780

Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility

Author keywords

Anisotropic network model; Docking minimization; Induced fit; Protein protein complex formation; Protein protein interaction

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; ARF1GTPASE; BACTERIAL PROTEIN; BINDING PROTEIN; DOCKING PROTEIN; GUANOSINE TRIPHOSPHATASE; HEMK ENZYME; LIGASE; MEMBRANE PROTEIN; METHYLTRANSFERASE; ORIGIN RECOGNITION COMPLEX; PROTEIN ARFBD; PROTEIN HIP2; PROTEIN ORC1; PROTEIN PAL; PROTEIN RF1; PROTEIN SIR1; PROTEIN TOLB; PROTEIN UBC9; RELEASING FACTOR; SILENT INFORMATION REGULATOR PROTEIN; UNCLASSIFIED DRUG;

EID: 36749035257     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21735     Document Type: Conference Paper
Times cited : (47)

References (33)
  • 1
    • 0037093640 scopus 로고    scopus 로고
    • Janin J. Welcome to CAPRI; a critical assessment of predicted interactions. Proteins 2002;47:257.
    • Janin J. Welcome to CAPRI; a critical assessment of predicted interactions. Proteins 2002;47:257.
  • 2
    • 1842861590 scopus 로고    scopus 로고
    • Prediction of protein-protein interactions: The CAPRI experiment, its evaluation and implications
    • Wodak SJ, Mendez R. Prediction of protein-protein interactions: the CAPRI experiment, its evaluation and implications. Curr Opin Struct Biol 2004;14:242-249.
    • (2004) Curr Opin Struct Biol , vol.14 , pp. 242-249
    • Wodak, S.J.1    Mendez, R.2
  • 3
    • 21644469377 scopus 로고    scopus 로고
    • Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures
    • Mendez R, Leplae R, Lensink MF, Wodak SJ. Assessment of CAPRI predictions in rounds 3-5 shows progress in docking procedures. Proteins 2005;60:150-169.
    • (2005) Proteins , vol.60 , pp. 150-169
    • Mendez, R.1    Leplae, R.2    Lensink, M.F.3    Wodak, S.J.4
  • 4
    • 0038583687 scopus 로고    scopus 로고
    • Protein-protein docking with a reduced protein model accounting for side-chain flexibility
    • Zacharias M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci 2003;12:1271-1282.
    • (2003) Protein Sci , vol.12 , pp. 1271-1282
    • Zacharias, M.1
  • 5
    • 21644435306 scopus 로고    scopus 로고
    • ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
    • Zacharias M. ATTRACT: protein-protein docking in CAPRI using a reduced protein model. Proteins 2005;60:252-256.
    • (2005) Proteins , vol.60 , pp. 252-256
    • Zacharias, M.1
  • 6
    • 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
  • 7
    • 1542316339 scopus 로고    scopus 로고
    • Rapid Protein-ligand docking including soft degrees of freedom from molecular dynamics simulations to account for protein flexibility: FK506 binding to FKBP binding protein as an example
    • Zacharias M. Rapid Protein-ligand docking including soft degrees of freedom from molecular dynamics simulations to account for protein flexibility: FK506 binding to FKBP binding protein as an example. Proteins 2004;54:759-767.
    • (2004) Proteins , vol.54 , pp. 759-767
    • Zacharias, M.1
  • 8
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for protein deformability during protein-protein and protein-ligand docking
    • May A, Zacharias M. Accounting for protein deformability during protein-protein and protein-ligand docking. Biochim Biophys Acta 2005;1754:225-231.
    • (2005) Biochim Biophys Acta , vol.1754 , pp. 225-231
    • May, A.1    Zacharias, M.2
  • 10
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter atomic analysis
    • Tirion MM. Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys Rev Lett 1996;77:1905-1908.
    • (1996) Phys Rev Lett , vol.77 , pp. 1905-1908
    • Tirion, M.M.1
  • 11
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar I, Atilgan AR, Erman B. Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. Fold Des 1997;2:173-181.
    • (1997) Fold Des , vol.2 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 12
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • Hinsen K. Analysis of domain motions by approximate normal mode calculations. Proteins 1998;33:417-429.
    • (1998) Proteins , vol.33 , pp. 417-429
    • Hinsen, K.1
  • 13
    • 0035044995 scopus 로고    scopus 로고
    • Conformational change of proteins arising from normal mode calculations
    • Tama F, Sanejouand YH. Conformational change of proteins arising from normal mode calculations. Protein Eng 2001;14:1-6.
    • (2001) Protein Eng , vol.14 , pp. 1-6
    • Tama, F.1    Sanejouand, Y.H.2
  • 14
    • 30044434744 scopus 로고    scopus 로고
    • Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
    • Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci USA 2005;102:18908-18913.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 18908-18913
    • Tobi, D.1    Bahar, I.2
  • 15
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • Bahar I, Rader EJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol 2005;15:586-592.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 586-592
    • Bahar, I.1    Rader, E.J.2
  • 16
    • 23344454719 scopus 로고    scopus 로고
    • Refinement of docked protein-ligand and protein-DNA structures using low-frequency normal mode amplitude optimization
    • Lindahl E, Delarue M. Refinement of docked protein-ligand and protein-DNA structures using low-frequency normal mode amplitude optimization. Nucleic Acids Res 2005;33:4496-4506.
    • (2005) Nucleic Acids Res , vol.33 , pp. 4496-4506
    • Lindahl, E.1    Delarue, M.2
  • 17
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex N, Peitsch MC. SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis 1997;18:2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 18
    • 36749036564 scopus 로고    scopus 로고
    • Case D, Pearlman DA, Caldwell JW, Cheatham III, TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. Amber 8. University of California, 2003, San Francisco.
    • Case D, Pearlman DA, Caldwell JW, Cheatham III, TE, Ross WS, Simmerling CL, Darden TA, Merz KM, Stanton RV, Cheng AL, Vincent JJ, Crowley M, Tsui V, Radmer RJ, Duan Y, Pitera J, Massova I, Seibel GL, Singh UC, Weiner PK, Kollman PA. Amber 8. University of California, 2003, San Francisco.
  • 19
    • 0032840382 scopus 로고    scopus 로고
    • Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis
    • Frolova LY, Tsivkovskii RY, Sivolobova GF, Oparina NY, Serpinsky OI, Blinov VM, Tatkov SI, Kisselev LL. Mutations in the highly conserved GGQ motif of class 1 polypeptide release factors abolish ability of human eRF1 to trigger peptidyl-tRNA hydrolysis. RNA 1999;5:1014-1020.
    • (1999) RNA , vol.5 , pp. 1014-1020
    • Frolova, L.Y.1    Tsivkovskii, R.Y.2    Sivolobova, G.F.3    Oparina, N.Y.4    Serpinsky, O.I.5    Blinov, V.M.6    Tatkov, S.I.7    Kisselev, L.L.8
  • 21
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede T, Kopp J, Guex N, Peitsch MC. SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res 2003;31:3381-3385.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 22
    • 33644843079 scopus 로고    scopus 로고
    • Accounting for loop flexibility during protein-protein docking
    • Bastard K, Prevost C, Zacharias M. Accounting for loop flexibility during protein-protein docking. Proteins 2006;62:956-969.
    • (2006) Proteins , vol.62 , pp. 956-969
    • Bastard, K.1    Prevost, C.2    Zacharias, M.3
  • 23
    • 20844445832 scopus 로고    scopus 로고
    • Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing
    • Hou Z, Bernstein D, Fox CA, Keck JL. Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 2005;102:8489-8494.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 8489-8494
    • Hou, Z.1    Bernstein, D.2    Fox, C.A.3    Keck, J.L.4
  • 24
    • 0037009519 scopus 로고    scopus 로고
    • Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing
    • Zhang Z, Hayashi MK, Merkel O, Stillman B, Xu RM. Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. EMBO J 2002;21:4600-4611.
    • (2002) EMBO J , vol.21 , pp. 4600-4611
    • Zhang, Z.1    Hayashi, M.K.2    Merkel, O.3    Stillman, B.4    Xu, R.M.5
  • 25
    • 0032944877 scopus 로고    scopus 로고
    • A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with Orc1 protein in Saccharomyces cerevisiae
    • Gardner KA, Rine J, Fox CA. A region of the Sir1 protein dedicated to recognition of a silencer and required for interaction with Orc1 protein in Saccharomyces cerevisiae. Genetics 1999;151:31-44.
    • (1999) Genetics , vol.151 , pp. 31-44
    • Gardner, K.A.1    Rine, J.2    Fox, C.A.3
  • 26
    • 34247473840 scopus 로고    scopus 로고
    • Molecular mimicry enables competitive recruitment by natively disordered protein
    • Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by natively disordered protein. J Am Chem Soc 2007;129:4800-4807.
    • (2007) J Am Chem Soc , vol.129 , pp. 4800-4807
    • Bonsor, D.A.1    Grishkovskaya, I.2    Dodson, E.J.3    Kleanthous, C.4
  • 29
    • 0033966170 scopus 로고    scopus 로고
    • Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction
    • Ray MC, Germon P, Vianney A, Portalier R, Lazzaroni JC. Identification by genetic suppression of Escherichia coli TolB residues important for TolB-Pal interaction. J Bacteriol 2000;182:821-824.
    • (2000) J Bacteriol , vol.182 , pp. 821-824
    • Ray, M.C.1    Germon, P.2    Vianney, A.3    Portalier, R.4    Lazzaroni, J.C.5
  • 30
    • 1242342946 scopus 로고    scopus 로고
    • Deletion analyses of the peptidoglycan-associated lipoprotein Pal reveals three independent binding sequences including a TolA box
    • Cascales E, Lloubes R. Deletion analyses of the peptidoglycan-associated lipoprotein Pal reveals three independent binding sequences including a TolA box. Mol Microbiol 2004;51:873-885.
    • (2004) Mol Microbiol , vol.51 , pp. 873-885
    • Cascales, E.1    Lloubes, R.2
  • 32
    • 33846227108 scopus 로고    scopus 로고
    • Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential
    • Kannan S, Zacharias M. Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing-potential. Proteins 2007;66:697-706.
    • (2007) Proteins , vol.66 , pp. 697-706
    • Kannan, S.1    Zacharias, M.2
  • 33
    • 26444587477 scopus 로고    scopus 로고
    • Refinement of protein cores and protein-peptide interfaces using a potential scaling approach
    • Riemann N, Zacharias M. Refinement of protein cores and protein-peptide interfaces using a potential scaling approach. Protein Eng 2005;18:465-476.
    • (2005) Protein Eng , vol.18 , pp. 465-476
    • Riemann, N.1    Zacharias, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.