메뉴 건너뛰기




Volumn 69, Issue 4, 2007, Pages 758-763

RosettaDock in CAPRI rounds 6-12

Author keywords

CAPRI; Flexible backbone docking; Homology docking; Loop modeling; Monte Carlo minimization

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 1; BACTERIAL PROTEIN; BINDING PROTEIN; DOCKING PROTEIN; HEMK ENZYME; HOMODIMER; LIGASE; MEMBRANE PROTEIN; METHYLTRANSFERASE; MONOMER; 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; UBIQUITIN PROTEIN LIGASE NEDD4; UNCLASSIFIED DRUG;

EID: 36749066580     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.21684     Document Type: Conference Paper
Times cited : (30)

References (43)
  • 2
    • 1242270553 scopus 로고    scopus 로고
    • Protein-protein docking: Is the glass half-full or half-empty?
    • Vajda S, Camacho CJ. Protein-protein docking: is the glass half-full or half-empty? Trends Biotechnol 2004;22:110-116.
    • (2004) Trends Biotechnol , vol.22 , pp. 110-116
    • Vajda, S.1    Camacho, C.J.2
  • 4
    • 0036606483 scopus 로고    scopus 로고
    • Principles of docking: An overview of search algorithms and a guide to scoring functions
    • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: an overview of search algorithms and a guide to scoring functions. Proteins 2002;47:409-443.
    • (2002) Proteins , vol.47 , pp. 409-443
    • Halperin, I.1    Ma, B.2    Wolfson, H.3    Nussinov, R.4
  • 6
    • 21644487998 scopus 로고    scopus 로고
    • The targets of CAPRI rounds 3-5
    • Janin J. The targets of CAPRI rounds 3-5. Proteins 2005;60:170-175.
    • (2005) Proteins , vol.60 , pp. 170-175
    • Janin, J.1
  • 7
    • 0038021436 scopus 로고    scopus 로고
    • Assessment of blind predictions of protein-protein interactions: Current status of docking methods
    • Mendez R, Leplae R, De Maria L, Wodak SJ. Assessment of blind predictions of protein-protein interactions: current status of docking methods. Proteins 2003;52:51-67.
    • (2003) Proteins , vol.52 , pp. 51-67
    • Mendez, R.1    Leplae, R.2    De Maria, L.3    Wodak, S.J.4
  • 8
    • 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
  • 9
    • 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
  • 10
    • 0038161052 scopus 로고    scopus 로고
    • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations
    • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. J Mol Biol 2003;331:281-299.
    • (2003) J Mol Biol , vol.331 , pp. 281-299
    • Gray, J.J.1    Moughon, S.2    Wang, C.3    Schueler-Furman, O.4    Kuhlman, B.5    Rohl, C.A.6    Baker, D.7
  • 11
    • 17744364070 scopus 로고    scopus 로고
    • Improved side-chain modeling for protein-protein docking
    • Wang C, Schueler-Furman O, Baker D. Improved side-chain modeling for protein-protein docking. Protein Sci 2005;14:1328-1339.
    • (2005) Protein Sci , vol.14 , pp. 1328-1339
    • Wang, C.1    Schueler-Furman, O.2    Baker, D.3
  • 12
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li Z, Scheraga HA. Monte Carlo-minimization approach to the multiple-minima problem in protein folding. Proc Natl Acad Sci USA 1987;84:6611-6615.
    • (1987) Proc Natl Acad Sci USA , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 13
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins 1999;35:133-152.
    • (1999) Proteins , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 14
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T, Morozov AV, Baker D. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J Mol Biol 2003;326:1239-1259.
    • (2003) J Mol Biol , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 15
    • 21644459373 scopus 로고    scopus 로고
    • Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
    • Schueler-Furman O, Wang C, Baker D. Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005;60:187-194.
    • (2005) Proteins , vol.60 , pp. 187-194
    • Schueler-Furman, O.1    Wang, C.2    Baker, D.3
  • 16
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • Canutescu AA, Dunbrack RL, Jr. Cyclic coordinate descent: a robotics algorithm for protein loop closure. Protein Sci 2003;12: 963-972.
    • (2003) Protein Sci , vol.12 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 17
    • 2442449534 scopus 로고    scopus 로고
    • Modeling structurally variable regions in homologous proteins with rosetta
    • Rohl CA, Strauss CE, Chivian D, Baker D. Modeling structurally variable regions in homologous proteins with rosetta. Proteins 2004;55:656-677.
    • (2004) Proteins , vol.55 , pp. 656-677
    • Rohl, C.A.1    Strauss, C.E.2    Chivian, D.3    Baker, D.4
  • 18
    • 33751118503 scopus 로고    scopus 로고
    • Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation
    • Bradley P, Baker D. Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins 2006;65:922-929.
    • (2006) Proteins , vol.65 , pp. 922-929
    • Bradley, P.1    Baker, D.2
  • 19
    • 0037084101 scopus 로고    scopus 로고
    • The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors
    • Heurgue-Hamard V, Champ S, Engstrom A, Ehrenberg M, Buckingham RH. The hemK gene in Escherichia coli encodes the N(5)-glutamine methyltransferase that modifies peptide release factors. EMBO J 2002;21:769-778.
    • (2002) EMBO J , vol.21 , pp. 769-778
    • Heurgue-Hamard, V.1    Champ, S.2    Engstrom, A.3    Ehrenberg, M.4    Buckingham, R.H.5
  • 20
    • 3042513877 scopus 로고    scopus 로고
    • Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase
    • Yang Z, Shipman L, Zhang M, Anton BP, Roberts RJ, Cheng X. Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase. J Mol Biol 2004;340:695-706.
    • (2004) J Mol Biol , vol.340 , pp. 695-706
    • Yang, Z.1    Shipman, L.2    Zhang, M.3    Anton, B.P.4    Roberts, R.J.5    Cheng, X.6
  • 21
    • 0038629269 scopus 로고    scopus 로고
    • Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase
    • Schubert HL, Phillips JD, Hill CP. Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase. Biochemistry 2003;42:5592-5599.
    • (2003) Biochemistry , vol.42 , pp. 5592-5599
    • Schubert, H.L.1    Phillips, J.D.2    Hill, C.P.3
  • 25
    • 34247473840 scopus 로고    scopus 로고
    • Molecular mimicry enables competitive recruitment by a natively disordered protein
    • Bonsor DA, Grishkovskaya I, Dodson EJ, Kleanthous C. Molecular mimicry enables competitive recruitment by a 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
  • 26
    • 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
  • 27
    • 20844445832 scopus 로고    scopus 로고
    • Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing
    • Hou Z, Bernstein DA, 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.A.2    Fox, C.A.3    Keck, J.L.4
  • 28
    • 0346725950 scopus 로고    scopus 로고
    • The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain
    • Bose ME, McConnell KH, Gardner-Aukema KA, Muller U, Weinreich M, Keck JL, Fox CA. The origin recognition complex and Sir4 protein recruit Sir1p to yeast silent chromatin through independent interactions requiring a common Sir1p domain. Mol Cell Biol 2004;24:774-786.
    • (2004) Mol Cell Biol , vol.24 , pp. 774-786
    • Bose, M.E.1    McConnell, K.H.2    Gardner-Aukema, K.A.3    Muller, U.4    Weinreich, M.5    Keck, J.L.6    Fox, C.A.7
  • 30
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 1999;292:195-202.
    • (1999) J Mol Biol , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 32
    • 27944510194 scopus 로고    scopus 로고
    • Membrane recruitment of effector proteins by Arf and Rab GTPases
    • Kawasaki M, Nakayama K, Wakatsuki S. Membrane recruitment of effector proteins by Arf and Rab GTPases. Curr Opin Struct Biol 2005;15:681-689.
    • (2005) Curr Opin Struct Biol , vol.15 , pp. 681-689
    • Kawasaki, M.1    Nakayama, K.2    Wakatsuki, S.3
  • 33
    • 0034650563 scopus 로고    scopus 로고
    • The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9
    • Carr S, Penfold CN, Bamford V, James R, Hemmings AM. The structure of TolB, an essential component of the tol-dependent translocation system, and its protein-protein interaction with the translocation domain of colicin E9. Structure 2000;8:57-66.
    • (2000) Structure , vol.8 , pp. 57-66
    • Carr, S.1    Penfold, C.N.2    Bamford, V.3    James, R.4    Hemmings, A.M.5
  • 34
    • 36749038768 scopus 로고    scopus 로고
    • MAD structure of the periplasmic domain of the E. coli pal protein
    • to be published
    • Abergel C, Walburger A, Bouveret E, Claverie JM. MAD structure of the periplasmic domain of the E. coli pal protein, to be published.
    • Abergel, C.1    Walburger, A.2    Bouveret, E.3    Claverie, J.M.4
  • 35
    • 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
  • 36
    • 0344631755 scopus 로고    scopus 로고
    • Bouveret E, Benedetti H, Rigal A, Loret E, Lazdunski C. In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions. J Bacteriol 1999;181:6306-6311.
    • Bouveret E, Benedetti H, Rigal A, Loret E, Lazdunski C. In vitro characterization of peptidoglycan-associated lipoprotein (PAL)-peptidoglycan and PAL-TolB interactions. J Bacteriol 1999;181:6306-6311.
  • 37
    • 0031848939 scopus 로고    scopus 로고
    • TolB protein of Escherichia coli K-12 interacts with the outer membrane peptidoglycan-associated proteins Pal, Lpp and OmpA
    • Clavel T, Germon P, Vianney A, Portalier R, Lazzaroni JC. TolB protein of Escherichia coli K-12 interacts with the outer membrane peptidoglycan-associated proteins Pal, Lpp and OmpA. Mol Microbiol 1998;29:359-367.
    • (1998) Mol Microbiol , vol.29 , pp. 359-367
    • Clavel, T.1    Germon, P.2    Vianney, A.3    Portalier, R.4    Lazzaroni, J.C.5
  • 39
    • 0030772385 scopus 로고    scopus 로고
    • Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system
    • Tong H, Hateboer G, Perrakis A, Bernards R, Sixma TK. Crystal structure of murine/human Ubc9 provides insight into the variability of the ubiquitin-conjugating system. J Biol Chem 1997;272: 21381-21387.
    • (1997) J Biol Chem , vol.272 , pp. 21381-21387
    • Tong, H.1    Hateboer, G.2    Perrakis, A.3    Bernards, R.4    Sixma, T.K.5
  • 43
    • 0037093643 scopus 로고    scopus 로고
    • Docking unbound proteins using shape complementarity, desolvation, and electrostatics
    • Chen R, Weng Z. Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins 2002;47:281-294.
    • (2002) Proteins , vol.47 , pp. 281-294
    • Chen, R.1    Weng, Z.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.