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Volumn 11, Issue , 2010, Pages

Analysis of protein-protein docking decoys using interaction fingerprints: Application to the reconstruction of CaM-ligand complexes

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONAL CHANGE; CYCLIC NUCLEOTIDE; FINGERPRINT METHOD; MEASURING SIMILARITIES; PROTEIN STRUCTURES; PROTEIN-PROTEIN COMPLEXES; PROTEIN-PROTEIN DOCKING; STRUCTURAL SIMILARITY;

EID: 77951965443     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-236     Document Type: Article
Times cited : (8)

References (27)
  • 1
    • 27144464910 scopus 로고    scopus 로고
    • Flexible nets: the roles of intrinsic disorder in protein interaction networks
    • 10.1111/j.1742-4658.2005.04948.x, 16218947
    • Dunker AK, Cortese MS, Romero P, Iakoucheva LM, Uversky VN. Flexible nets: the roles of intrinsic disorder in protein interaction networks. FEBS Journal 2005, 272:5129-5148. 10.1111/j.1742-4658.2005.04948.x, 16218947.
    • (2005) FEBS Journal , vol.272 , pp. 5129-5148
    • Dunker, A.K.1    Cortese, M.S.2    Romero, P.3    Iakoucheva, L.M.4    Uversky, V.N.5
  • 2
    • 0034609791 scopus 로고    scopus 로고
    • The large-scale organization of metabolic networks
    • 10.1038/35036627, 11034217
    • Jeong H, Tombor B, Albert R, Oltvai ZN, BarabaÂsi AL. The large-scale organization of metabolic networks. Nature 2000, 407:651-654. 10.1038/35036627, 11034217.
    • (2000) Nature , vol.407 , pp. 651-654
    • Jeong, H.1    Tombor, B.2    Albert, R.3    Oltvai, Z.N.4    BarabaÂsi, A.L.5
  • 3
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • 10.1038/35075138, 11333967
    • Jeong H, Mason SP, Barabási AL, Oltvai ZN. Lethality and centrality in protein networks. Nature 2001, 411:41-42. 10.1038/35075138, 11333967.
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabási, A.L.3    Oltvai, Z.N.4
  • 4
    • 33645214608 scopus 로고    scopus 로고
    • Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks
    • Patil A, Nakamura H. Disordered domains and high surface charge confer hubs with the ability to interact with multiple proteins in interaction networks. FEBS Letter 2006, 580:2041-2045.
    • (2006) FEBS Letter , vol.580 , pp. 2041-2045
    • Patil, A.1    Nakamura, H.2
  • 5
    • 37549002450 scopus 로고    scopus 로고
    • Identification of transient hub proteins and the possible structural basis for their multiple interactions
    • 10.1110/ps.073196308, 2144588, 18156468
    • Higurashi M, Ishida T, Kinoshita K. Identification of transient hub proteins and the possible structural basis for their multiple interactions. Protein Sci 2008, 17:72-78. 10.1110/ps.073196308, 2144588, 18156468.
    • (2008) Protein Sci , vol.17 , pp. 72-78
    • Higurashi, M.1    Ishida, T.2    Kinoshita, K.3
  • 6
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for global protein deformability during protein-protein and protein-ligand docking
    • May A, Zacharias M. Accounting for global 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
  • 7
    • 36749057349 scopus 로고    scopus 로고
    • Implicit flexibility in protein docking: cross-docking and local refinement
    • 10.1002/prot.21698, 17671977
    • Król M, Chaleil RAG, Tournier AL, Bates PA. Implicit flexibility in protein docking: cross-docking and local refinement. Proteins 2007, 69:750-757. 10.1002/prot.21698, 17671977.
    • (2007) Proteins , vol.69 , pp. 750-757
    • Król, M.1    Chaleil, R.A.G.2    Tournier, A.L.3    Bates, P.A.4
  • 8
    • 36749006579 scopus 로고    scopus 로고
    • Docking and scoring protein complexes: CAPRI 3rd edition
    • 10.1002/prot.21804, 17918726
    • Lensink MF, Méndez R, Wodak SJ. Docking and scoring protein complexes: CAPRI 3rd edition. Proteins 2007, 69:704-718. 10.1002/prot.21804, 17918726.
    • (2007) Proteins , vol.69 , pp. 704-718
    • Lensink, M.F.1    Méndez, R.2    Wodak, S.J.3
  • 9
    • 36749035257 scopus 로고    scopus 로고
    • Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility
    • 10.1002/prot.21735, 17803217
    • May A, Zacharias M. Protein-protein docking in CAPRI using ATTRACT to account for global and local flexibility. Proteins 2007, 69:774-780. 10.1002/prot.21735, 17803217.
    • (2007) Proteins , vol.69 , pp. 774-780
    • May, A.1    Zacharias, M.2
  • 10
    • 38549097715 scopus 로고    scopus 로고
    • Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking
    • 10.1002/prot.21579, 17729269
    • May A, Zacharias M. Energy minimization in low-frequency normal modes to efficiently allow for global flexibility during systematic protein-protein docking. Proteins 2008, 70:794-809. 10.1002/prot.21579, 17729269.
    • (2008) Proteins , vol.70 , pp. 794-809
    • May, A.1    Zacharias, M.2
  • 11
    • 15244355250 scopus 로고    scopus 로고
    • The relationship between the flexibility of proteins and their conformational states on forming protein-porotein complexes with an application to protein-protein docking
    • 10.1016/j.jmb.2005.01.058, 15784265
    • Smith GR, Sternberg MJE, Bates PA. The relationship between the flexibility of proteins and their conformational states on forming protein-porotein complexes with an application to protein-protein docking. J Mol Biol 2005, 347:1077-1101. 10.1016/j.jmb.2005.01.058, 15784265.
    • (2005) J Mol Biol , vol.347 , pp. 1077-1101
    • Smith, G.R.1    Sternberg, M.J.E.2    Bates, P.A.3
  • 12
    • 0038185195 scopus 로고    scopus 로고
    • Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking
    • 10.1093/proeng/gzg021, 12702797
    • Heifetz A, Eisenstein M. Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Engineering 2003, 16:179-185. 10.1093/proeng/gzg021, 12702797.
    • (2003) Protein Engineering , vol.16 , pp. 179-185
    • Heifetz, A.1    Eisenstein, M.2
  • 13
    • 21644440105 scopus 로고    scopus 로고
    • Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI
    • Carter P, Lesk VI, Islam SA, Sternberg MJE. Protein-protein docking using 3D-Dock in rounds 3, 4, and 5 of CAPRI. Proteins 2006, 60:281-288.
    • (2006) Proteins , vol.60 , pp. 281-288
    • Carter, P.1    Lesk, V.I.2    Islam, S.A.3    Sternberg, M.J.E.4
  • 14
    • 0042622381 scopus 로고    scopus 로고
    • LGA: a method for finding 3D similarities in protein structures
    • Zemla A. LGA: a method for finding 3D similarities in protein structures. Nucleic Acid Research 2003, 31:3370-3374.
    • (2003) Nucleic Acid Research , vol.31 , pp. 3370-3374
    • Zemla, A.1
  • 15
    • 0346962971 scopus 로고    scopus 로고
    • Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions
    • 10.1021/jm030331x, 14711306
    • Deng Z, Chuaqui C, Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem 2004, 47:337-344. 10.1021/jm030331x, 14711306.
    • (2004) J Med Chem , vol.47 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 16
    • 33846933784 scopus 로고    scopus 로고
    • Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
    • 10.1021/ci600342e, 17238265
    • Marcou G, Rognan D. Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 2007, 47:195-207. 10.1021/ci600342e, 17238265.
    • (2007) J Chem Inf Model , vol.47 , pp. 195-207
    • Marcou, G.1    Rognan, D.2
  • 17
    • 22144464877 scopus 로고    scopus 로고
    • Structure of calmodulin comlexed with an olfactory CNG channel fragment and role of central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family
    • 10.1007/s10858-005-0165-1, 15803393
    • Contessa GM, Orsale M, Melino S, Torre V, Paci M, Desideri A, Cicero DO. Structure of calmodulin comlexed with an olfactory CNG channel fragment and role of central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family. J Biomol NMR 2005, 31:185-199. 10.1007/s10858-005-0165-1, 15803393.
    • (2005) J Biomol NMR , vol.31 , pp. 185-199
    • Contessa, G.M.1    Orsale, M.2    Melino, S.3    Torre, V.4    Paci, M.5    Desideri, A.6    Cicero, D.O.7
  • 18
    • 0032834002 scopus 로고    scopus 로고
    • A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase
    • 10.1038/12271, 10467092
    • Osawa M, Tokumitsu H, Swindells MB, Kurihara H, Orita M, Shibanuma T, Furuya T, Ikura M. A novel target recognition revealed by calmodulin in complex with Ca2+-calmodulin-dependent kinase kinase. Nat Struct Biol 1999, 6:819-924. 10.1038/12271, 10467092.
    • (1999) Nat Struct Biol , vol.6 , pp. 819-924
    • Osawa, M.1    Tokumitsu, H.2    Swindells, M.B.3    Kurihara, H.4    Orita, M.5    Shibanuma, T.6    Furuya, T.7    Ikura, M.8
  • 20
    • 0029160568 scopus 로고
    • Calcium-induced conformational transition revealed by the solution structure of apo calmodulin
    • 10.1038/nsb0995-758, 7552747
    • Zhang M, Tanaka T, Ikura M. Calcium-induced conformational transition revealed by the solution structure of apo calmodulin. Nat struct biol 1995, 2:758-767. 10.1038/nsb0995-758, 7552747.
    • (1995) Nat struct biol , vol.2 , pp. 758-767
    • Zhang, M.1    Tanaka, T.2    Ikura, M.3
  • 21
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: and initial-stage protein-docking algorithm
    • 10.1002/prot.10389, 12784371
    • Chen R, Li L, Weng Z. ZDOCK: and initial-stage protein-docking algorithm. Proteins 2003, 52:80-87. 10.1002/prot.10389, 12784371.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 22
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • 10.1002/prot.10092, 11948782
    • Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002, 47:281-294. 10.1002/prot.10092, 11948782.
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2
  • 23
    • 0042511005 scopus 로고    scopus 로고
    • A graph-theory algorithm for rapid protein side-chain prediction
    • 10.1110/ps.03154503, 2323997, 12930999
    • Canutescu AA, Shelenkov AA, Dunbrack RL. A graph-theory algorithm for rapid protein side-chain prediction. Protein Sci 2003, 12:2001-2014. 10.1110/ps.03154503, 2323997, 12930999.
    • (2003) Protein Sci , vol.12 , pp. 2001-2014
    • Canutescu, A.A.1    Shelenkov, A.A.2    Dunbrack, R.L.3
  • 24
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: reranking protein docking predictions with an optimized energy function
    • 10.1002/prot.21373, 17373710
    • Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007, 67:1078-1086. 10.1002/prot.21373, 17373710.
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 25
    • 0028922586 scopus 로고
    • LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions
    • 10.1093/protein/8.2.127, 7630882
    • Wallace AC, Laskowski RA, Thornton JM. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng 1995, 8:127-134. 10.1093/protein/8.2.127, 7630882.
    • (1995) Protein Eng , vol.8 , pp. 127-134
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 26
    • 58149411184 scopus 로고
    • Features of similarity
    • Tversky A. Features of similarity. Psychol Rev 1977, 84:327-352.
    • (1977) Psychol Rev , vol.84 , pp. 327-352
    • Tversky, A.1
  • 27
    • 0037835585 scopus 로고    scopus 로고
    • Analysis and display of the size dependence of chemical similarity coefficients
    • Holliday JD, Salim N, Whittle M, Willet P. Analysis and display of the size dependence of chemical similarity coefficients. J Chem Inf Comput Sci 2003, 43:819-828.
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 819-828
    • Holliday, J.D.1    Salim, N.2    Whittle, M.3    Willet, P.4


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