메뉴 건너뛰기




Volumn 78, Issue 15, 2010, Pages 3166-3173

Selection of near-native poses in CAPRI rounds 13-19

Author keywords

Interface prediction; Protein docking; Protein protein interaction

Indexed keywords

ADENOSINE DIPHOSPHATE RIBOSYLATION FACTOR 6; COLICIN; FORKHEAD ASSOCIATED DOMAIN KIF13B; FORKHEAD TRANSCRIPTION FACTOR; HOMODIMER; JANUS KINASE; JANUS KINASE INTERACTING PROTEIN 4; LEUCINE ZIPPER PROTEIN; NUCLEAR PROTEIN; PLEXIN; PROTEIN CENTAURIN ALPHA1; PROTEIN LZ2; PROTEIN RND1; PROTEIN TRM8; PROTEIN TRM82; S ADENOSYLMETHIONINE; SUBTILISIN; TRYPSIN; UNCLASSIFIED DRUG;

EID: 77957953575     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22772     Document Type: Article
Times cited : (9)

References (47)
  • 1
    • 0038526303 scopus 로고    scopus 로고
    • ZDOCK: an initial-stage protein-docking algorithm
    • Chen R, Li L, Weng Z. ZDOCK: an initial-stage protein-docking algorithm. Proteins 2003;52:80-87.
    • (2003) Proteins , vol.52 , pp. 80-87
    • Chen, R.1    Li, L.2    Weng, Z.3
  • 2
    • 33749020839 scopus 로고    scopus 로고
    • PIPER: an FFT-based protein docking program with pairwise potentials
    • Kozakov D, Brenke R, Comeau SR, Vajda S. PIPER: an FFT-based protein docking program with pairwise potentials. Proteins 2006;65: 392-406.
    • (2006) Proteins , vol.65 , pp. 392-406
    • Kozakov, D.1    Brenke, R.2    Comeau, S.R.3    Vajda, S.4
  • 3
    • 36749077465 scopus 로고    scopus 로고
    • Automatic prediction of protein interactions with large scale motion
    • Schneidman-Duhovny D, Nussinov R, Wolfson HJ. Automatic prediction of protein interactions with large scale motion. Proteins 2007;69:764-773.
    • (2007) Proteins , vol.69 , pp. 764-773
    • Schneidman-Duhovny, D.1    Nussinov, R.2    Wolfson, H.J.3
  • 4
    • 36749082073 scopus 로고    scopus 로고
    • A holistic approach to protein docking
    • Qin S, Zhou HX. A holistic approach to protein docking. Proteins 2007;69:743-749.
    • (2007) Proteins , vol.69 , pp. 743-749
    • Qin, S.1    Zhou, H.X.2
  • 5
    • 34248513078 scopus 로고    scopus 로고
    • ZRANK: reranking protein docking predictions with an optimized energy function
    • Pierce B, Weng Z. ZRANK: reranking protein docking predictions with an optimized energy function. Proteins 2007;67:1078-1086.
    • (2007) Proteins , vol.67 , pp. 1078-1086
    • Pierce, B.1    Weng, Z.2
  • 6
    • 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
  • 7
    • 0242299200 scopus 로고    scopus 로고
    • RDOCK: refinement of rigid-body protein docking predictions
    • Li L, Chen R, Weng Z. RDOCK: refinement of rigid-body protein docking predictions. Proteins 2003;53:693-707.
    • (2003) Proteins , vol.53 , pp. 693-707
    • Li, L.1    Chen, R.2    Weng, Z.3
  • 8
    • 55449101982 scopus 로고    scopus 로고
    • Protein docking by the underestimation of free energy funnels in the space of encounter complexes
    • Shen Y, Paschalidis I, Vakili P, Vajda S. Protein docking by the underestimation of free energy funnels in the space of encounter complexes. PLoS Comput Biol 2008;4:e1000191.
    • (2008) PLoS Comput Biol , vol.4
    • Shen, Y.1    Paschalidis, I.2    Vakili, P.3    Vajda, S.4
  • 9
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou HX, Shan Y. Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins 2001;44:336-343.
    • (2001) Proteins , vol.44 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.2
  • 11
    • 34548751368 scopus 로고    scopus 로고
    • meta-PPISP: a meta web server for protein-protein interaction site prediction
    • Qin S, Zhou HX. meta-PPISP: a meta web server for protein-protein interaction site prediction. Bioinformatics 2007;23:3386-3387.
    • (2007) Bioinformatics , vol.23 , pp. 3386-3387
    • Qin, S.1    Zhou, H.X.2
  • 12
    • 24344484686 scopus 로고    scopus 로고
    • Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data
    • Chen H, Zhou HX. Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. Proteins 2005;61:21-35.
    • (2005) Proteins , vol.61 , pp. 21-35
    • Chen, H.1    Zhou, H.X.2
  • 13
    • 33747150197 scopus 로고    scopus 로고
    • Protein binding site prediction using an empirical scoring function
    • Liang S, Zhang C, Liu S, Zhou Y. Protein binding site prediction using an empirical scoring function. Nucleic Acids Res 2006;34: 3698-3707.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3698-3707
    • Liang, S.1    Zhang, C.2    Liu, S.3    Zhou, Y.4
  • 14
    • 1842526090 scopus 로고    scopus 로고
    • ProMate: a structure based prediction program to identify the location of protein-protein binding sites
    • Neuvirth H, Raz R, Schreiber G. ProMate: a structure based prediction program to identify the location of protein-protein binding sites. J Mol Biol 2004;338:181-199.
    • (2004) J Mol Biol , vol.338 , pp. 181-199
    • Neuvirth, H.1    Raz, R.2    Schreiber, G.3
  • 15
    • 17444385658 scopus 로고    scopus 로고
    • M-ZDOCK: a grid-based approach for Cn symmetric multimer docking
    • Pierce B, Tong W, Weng Z. M-ZDOCK: a grid-based approach for Cn symmetric multimer docking. Bioinformatics 2005;21:1472-1478.
    • (2005) Bioinformatics , vol.21 , pp. 1472-1478
    • Pierce, B.1    Tong, W.2    Weng, Z.3
  • 16
    • 18844462557 scopus 로고    scopus 로고
    • FastContact: rapid estimate of contact and binding free energies
    • Camacho CJ, Zhang C. FastContact: rapid estimate of contact and binding free energies. Bioinformatics 2005;21:2534-2536.
    • (2005) Bioinformatics , vol.21 , pp. 2534-2536
    • Camacho, C.J.1    Zhang, C.2
  • 17
    • 1942423619 scopus 로고    scopus 로고
    • MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology
    • Feig M, Karanicolas J, Brooks CL, III. MMTSB tool set: enhanced sampling and multiscale modeling methods for applications in structural biology. J Mol Graph Model 2004;22:377-395.
    • (2004) J Mol Graph Model , vol.22 , pp. 377-395
    • Feig, M.1    Karanicolas, J.2    Brooks C.L. III3
  • 18
    • 0037442962 scopus 로고    scopus 로고
    • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information
    • Dominguez C, Boelens R, Bonvin AM. HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 2003;125:1731-1737.
    • (2003) J Am Chem Soc , vol.125 , pp. 1731-1737
    • Dominguez, C.1    Boelens, R.2    Bonvin, A.M.3
  • 20
    • 17944373789 scopus 로고    scopus 로고
    • Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis
    • Purta E, van Vliet F, Tricot C, De Bie LG, Feder M, Skowronek K, Droogmans L, Bujnicki JM. Sequence-structure-function relationships of a tRNA (m7G46) methyltransferase studied by homology modeling and site-directed mutagenesis. Proteins 2005;59:482-488.
    • (2005) Proteins , vol.59 , pp. 482-488
    • Purta, E.1    van Vliet, F.2    Tricot, C.3    De Bie, L.G.4    Feder, M.5    Skowronek, K.6    Droogmans, L.7    Bujnicki, J.M.8
  • 21
    • 0036795285 scopus 로고    scopus 로고
    • Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA
    • Alexandrov A, Martzen MR, Phizicky EM. Two proteins that form a complex are required for 7-methylguanosine modification of yeast tRNA. Rna 2002;8:1253-1266.
    • (2002) Rna , vol.8 , pp. 1253-1266
    • Alexandrov, A.1    Martzen, M.R.2    Phizicky, E.M.3
  • 22
    • 17844373810 scopus 로고    scopus 로고
    • tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p
    • Alexandrov A, Grayhack EJ, Phizicky EM. tRNA m7G methyltransferase Trm8p/Trm82p: evidence linking activity to a growth phenotype and implicating Trm82p in maintaining levels of active Trm8p. Rna 2005;11:821-830.
    • (2005) Rna , vol.11 , pp. 821-830
    • Alexandrov, A.1    Grayhack, E.J.2    Phizicky, E.M.3
  • 23
    • 37549021146 scopus 로고    scopus 로고
    • Binding of Rac1. Rnd1, and Rho D to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain
    • Tong Y, Chugha P, Hota PK, Alviani RS, Li M, Tempel W, Shen L, Park HW, Buck M. Binding of Rac1. Rnd1, and Rho D to a novel Rho GTPase interaction motif destabilizes dimerization of the plexin-B1 effector domain J Biol Chem 2007;282:37215-37224.
    • (2007) J Biol Chem , vol.282 , pp. 37215-37224
    • Tong, Y.1    Chugha, P.2    Hota, P.K.3    Alviani, R.S.4    Li, M.5    Tempel, W.6    Shen, L.7    Park, H.W.8    Buck, M.9
  • 24
    • 0038491273 scopus 로고    scopus 로고
    • Direct interaction of Rnd1 with Plexin-B1 regulates PDZ-RhoGEF-mediated Rho activation by Plexin-B1 and induces cell contraction in COS-7 cells
    • Oinuma I, Katoh H, Harada A, Negishi M. Direct interaction of Rnd1 with Plexin-B1 regulates PDZ-RhoGEF-mediated Rho activation by Plexin-B1 and induces cell contraction in COS-7 cells. J Biol Chem 2003;278:25671-25677.
    • (2003) J Biol Chem , vol.278 , pp. 25671-25677
    • Oinuma, I.1    Katoh, H.2    Harada, A.3    Negishi, M.4
  • 26
    • 45649084937 scopus 로고    scopus 로고
    • Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition
    • Micheelsen PO, Vevodova J, De Maria L, Ostergaard PR, Friis EP, Wilson K, Skjot M. Structural and mutational analyses of the interaction between the barley alpha-amylase/subtilisin inhibitor and the subtilisin savinase reveal a novel mode of inhibition. J Mol Biol 2008;380:681-690.
    • (2008) J Mol Biol , vol.380 , pp. 681-690
    • Micheelsen, P.O.1    Vevodova, J.2    De Maria, L.3    Ostergaard, P.R.4    Friis, E.P.5    Wilson, K.6    Skjot, M.7
  • 27
    • 0028168285 scopus 로고
    • Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5.
    • Lange G, Betzel C, Branner S, Wilson KS. Crystallographic studies of Savinase, a subtilisin-like proteinase, at pH 10.5. Eur J Biochem 1994;224:507-518.
    • (1994) Eur J Biochem , vol.224 , pp. 507-518
    • Lange, G.1    Betzel, C.2    Branner, S.3    Wilson, K.S.4
  • 28
    • 0032524130 scopus 로고    scopus 로고
    • Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution
    • Vallee F, Kadziola A, Bourne Y, Juy M, Rodenburg KW, Svensson B, Haser R. Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution. Structure 1998;6:649-659.
    • (1998) Structure , vol.6 , pp. 649-659
    • Vallee, F.1    Kadziola, A.2    Bourne, Y.3    Juy, M.4    Rodenburg, K.W.5    Svensson, B.6    Haser, R.7
  • 29
    • 17644379997 scopus 로고    scopus 로고
    • Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor
    • Bonsager BC, Nielsen PK, Abou Hachem M, Fukuda K, Praetorius-Ibba M, Svensson B. Mutational analysis of target enzyme recognition of the beta-trefoil fold barley alpha-amylase/subtilisin inhibitor. J Biol Chem 2005;280:14855-14864.
    • (2005) J Biol Chem , vol.280 , pp. 14855-14864
    • Bonsager, B.C.1    Nielsen, P.K.2    Abou Hachem, M.3    Fukuda, K.4    Praetorius-Ibba, M.5    Svensson, B.6
  • 30
    • 0025812630 scopus 로고
    • Refined crystal structure of the complex of subtilisin BPN0 and Streptomyces subtilisin inhibitor at 1-8 Åresolution
    • Takeuchi Y, Satow Y, Nakamura KT, Mitsui Y. Refined crystal structure of the complex of subtilisin BPN0 and Streptomyces subtilisin inhibitor at 1-8 Åresolution. J Mol Biol 1991;221:309-325.
    • (1991) J Mol Biol , vol.221 , pp. 309-325
    • Takeuchi, Y.1    Satow, Y.2    Nakamura, K.T.3    Mitsui, Y.4
  • 31
    • 34547929767 scopus 로고    scopus 로고
    • Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II)
    • Lebars I, Husson C, Yoshizawa S, Douthwaite S, Fourmy D. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmA(II). J Mol Biol 2007;372:525-534.
    • (2007) J Mol Biol , vol.372 , pp. 525-534
    • Lebars, I.1    Husson, C.2    Yoshizawa, S.3    Douthwaite, S.4    Fourmy, D.5
  • 32
    • 1642529580 scopus 로고    scopus 로고
    • Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site
    • Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione GT. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc Natl Acad Sci USA 2004;101:4041-4046.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 4041-4046
    • Das, K.1    Acton, T.2    Chiang, Y.3    Shih, L.4    Arnold, E.5    Montelione, G.T.6
  • 34
    • 1642523638 scopus 로고    scopus 로고
    • Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases
    • Pell G, Szabo L, Charnock SJ, Xie H, Gloster TM, Davies GJ, Gilbert HJ. Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases. J Biol Chem 2004;279:11777-11788.
    • (2004) J Biol Chem , vol.279 , pp. 11777-11788
    • Pell, G.1    Szabo, L.2    Charnock, S.J.3    Xie, H.4    Gloster, T.M.5    Davies, G.J.6    Gilbert, H.J.7
  • 37
    • 0842269776 scopus 로고    scopus 로고
    • Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1
    • Wu M, Lu L, Hong W, Song H. Structural basis for recruitment of GRIP domain golgin-245 by small GTPase Arl1. Nat Struct Mol Biol 2004;11:86-94.
    • (2004) Nat Struct Mol Biol , vol.11 , pp. 86-94
    • Wu, M.1    Lu, L.2    Hong, W.3    Song, H.4
  • 38
  • 40
    • 21044433466 scopus 로고    scopus 로고
    • Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B
    • (Part 11)
    • Venkateswarlu K, Hanada T, Chishti AH. Centaurin-alpha1 interacts directly with kinesin motor protein KIF13B. J Cell Sci 2005;118 (Part 11):2471-2484.
    • (2005) J Cell Sci , vol.118 , pp. 2471-2484
    • Venkateswarlu, K.1    Hanada, T.2    Chishti, A.H.3
  • 41
    • 70350355110 scopus 로고    scopus 로고
    • The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation
    • Bao R, Zhou CZ, Jiang C, Lin SX, Chi CW, Chen Y. The ternary structure of the double-headed arrowhead protease inhibitor API-A complexed with two trypsins reveals a novel reactive site conformation. J Biol Chem 2009;284:26676-26684.
    • (2009) J Biol Chem , vol.284 , pp. 26676-26684
    • Bao, R.1    Zhou, C.Z.2    Jiang, C.3    Lin, S.X.4    Chi, C.W.5    Chen, Y.6
  • 42
    • 0030794907 scopus 로고    scopus 로고
    • Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities
    • Scheidig AJ, Hynes TR, Pelletier LA, Wells JA, Kossiakoff AA. Crystal structures of bovine chymotrypsin and trypsin complexed to the inhibitor domain of Alzheimer's amyloid beta-protein precursor (APPI) and basic pancreatic trypsin inhibitor (BPTI): engineering of inhibitors with altered specificities. Protein Sci 1997;6: 1806-1824.
    • (1997) Protein Sci , vol.6 , pp. 1806-1824
    • Scheidig, A.J.1    Hynes, T.R.2    Pelletier, L.A.3    Wells, J.A.4    Kossiakoff, A.A.5
  • 44
    • 0030867940 scopus 로고    scopus 로고
    • Protein-protein interaction specificity of Im9 for the endonuclease toxin colicin E9 defined by homologue-scanning mutagenesis
    • Li W, Dennis CA, Moore GR, James R, Kleanthous C. Protein-protein interaction specificity of Im9 for the endonuclease toxin colicin E9 defined by homologue-scanning mutagenesis. J Biol Chem 1997;272:22253-22258.
    • (1997) J Biol Chem , vol.272 , pp. 22253-22258
    • Li, W.1    Dennis, C.A.2    Moore, G.R.3    James, R.4    Kleanthous, C.5
  • 45
    • 0032566286 scopus 로고    scopus 로고
    • Dual recognition and the role of specificity-determining residues in colicin E9 DNase-immunity protein interactions
    • Li W, Hamill SJ, Hemmings AM, Moore GR, James R, Kleanthous C. Dual recognition and the role of specificity-determining residues in colicin E9 DNase-immunity protein interactions. Biochemistry 1998;37:11771-11779.
    • (1998) Biochemistry , vol.37 , pp. 11771-11779
    • Li, W.1    Hamill, S.J.2    Hemmings, A.M.3    Moore, G.R.4    James, R.5    Kleanthous, C.6
  • 46
    • 77953593958 scopus 로고    scopus 로고
    • Self-association of TPR-domains: natural and engineered
    • Krachler AM, Sharma A, Kleanthous C. Self-association of TPR-domains: natural and engineered. Proteins 2010;78:2131-2143.
    • (2010) Proteins , vol.78 , pp. 2131-2143
    • Krachler, A.M.1    Sharma, A.2    Kleanthous, C.3
  • 47
    • 0037648552 scopus 로고    scopus 로고
    • Design of stable alpha-helical arrays from an idealized TPR motif
    • Main ER, Xiong Y, Cocco MJ, D'Andrea L, Regan L. Design of stable alpha-helical arrays from an idealized TPR motif. Structure 2003;11:497-508.
    • (2003) Structure , vol.11 , pp. 497-508
    • Main, E.R.1    Xiong, Y.2    Cocco, M.J.3    D'Andrea, L.4    Regan, L.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.