메뉴 건너뛰기




Volumn 84, Issue S1, 2016, Pages 34-50

Some of the most interesting CASP11 targets through the eyes of their authors

(24)  Kryshtafovych, Andriy a   Moult, John b   Baslé, Arnaud c   Burgin, Alex d   Craig, Timothy K e   Edwards, Robert A f,g   Fass, Deborah h   Hartmann, Marcus D i   Korycinski, Mateusz i   Lewis, Richard J c   Lorimer, Donald j   Lupas, Andrei N i   Newman, Janet k   Peat, Thomas S k   Piepenbrink, Kurt H l   Prahlad, Janani m   van Raaij, Mark J n   Rohwer, Forest f   Segall, Anca M f   Seguritan, Victor o   more..


Author keywords

CASP; NMR; protein structure prediction; X ray crystallography

Indexed keywords

PROTEIN;

EID: 84947982835     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.24942     Document Type: Article
Times cited : (16)

References (69)
  • 1
    • 84893021599 scopus 로고    scopus 로고
    • Critical assessment of methods of protein structure prediction (CASP) - round x
    • Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) - round x. Proteins 2014;82:1–6.
    • (2014) Proteins , vol.82 , pp. 1-6
    • Moult, J.1    Fidelis, K.2    Kryshtafovych, A.3    Schwede, T.4    Tramontano, A.5
  • 4
    • 84893010856 scopus 로고    scopus 로고
    • CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL
    • Kryshtafovych A, Monastyrskyy B, Fidelis K. CASP prediction center infrastructure and evaluation measures in CASP10 and CASP ROLL. Proteins 2014;82(Suppl 2):7–13.
    • (2014) Proteins , vol.82Suppl 2 , pp. 7-13
    • Kryshtafovych, A.1    Monastyrskyy, B.2    Fidelis, K.3
  • 5
    • 79955542589 scopus 로고    scopus 로고
    • The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron
    • Liu Y, Bauer SC, Imlay JA. The YaaA protein of the Escherichia coli OxyR regulon lessens hydrogen peroxide toxicity by diminishing the amount of intracellular unincorporated iron. J Bacteriol 2011;193:2186–2196.
    • (2011) J Bacteriol , vol.193 , pp. 2186-2196
    • Liu, Y.1    Bauer, S.C.2    Imlay, J.A.3
  • 6
    • 84884603324 scopus 로고    scopus 로고
    • Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era
    • Kamisetty H, Ovchinnikov S, Baker D. Assessing the utility of coevolution-based residue-residue contact predictions in a sequence- and structure-rich era. Proc Natl Acad Sci USA 2013;110:15674–15679.
    • (2013) Proc Natl Acad Sci USA , vol.110 , pp. 15674-15679
    • Kamisetty, H.1    Ovchinnikov, S.2    Baker, D.3
  • 7
    • 84899847547 scopus 로고    scopus 로고
    • Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information
    • Ovchinnikov S, Kamisetty H, Baker D. Robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information. eLife 2014;3:e02030.
    • (2014) eLife , vol.3
    • Ovchinnikov, S.1    Kamisetty, H.2    Baker, D.3
  • 9
    • 84872200290 scopus 로고    scopus 로고
    • The laminin family
    • Aumailley M. The laminin family. Cell Adhes Migr 2013;7:48–55.
    • (2013) Cell Adhes Migr , vol.7 , pp. 48-55
    • Aumailley, M.1
  • 11
    • 84944900695 scopus 로고    scopus 로고
    • domain structure resembles adhesion modules in ephrin receptor and other transmembrane glycoproteins
    • Laminin L4
    • Moran T, Gat Y, Fass D. Laminin L4 domain structure resembles adhesion modules in ephrin receptor and other transmembrane glycoproteins. FEBS J 2015;282(14): 2746–2757.
    • (2015) FEBS J , vol.282 , Issue.14 , pp. 2746-2757
    • Moran, T.1    Gat, Y.2    Fass, D.3
  • 12
    • 77954288774 scopus 로고    scopus 로고
    • Dali server: conservation mapping in 3D
    • –W
    • Holm L, Rosenstrom P. Dali server: conservation mapping in 3D. Nucleic Acids Res 2010;38:W545–W549.
    • (2010) Nucleic Acids Res , vol.38 , pp. W545-549
    • Holm, L.1    Rosenstrom, P.2
  • 14
    • 0029146393 scopus 로고
    • Adenovirus–an eternal archetype
    • Philipson L. Adenovirus–an eternal archetype. Curr Top Microbiol Immunol 1995;199:1–24.
    • (1995) Curr Top Microbiol Immunol , vol.199 , pp. 1-24
    • Philipson, L.1
  • 16
    • 84861540383 scopus 로고    scopus 로고
    • Latest insights on adenovirus structure and assembly
    • San Martin C. Latest insights on adenovirus structure and assembly. Viruses 2012;4:847–877.
    • (2012) Viruses , vol.4 , pp. 847-877
    • San Martin, C.1
  • 17
    • 84915745920 scopus 로고    scopus 로고
    • Crystal structure of the fibre head domain of the Atadenovirus snake adenovirus 1
    • Singh AK, Menendez-Conejero R, San Martin C, van Raaij MJ. Crystal structure of the fibre head domain of the Atadenovirus snake adenovirus 1. PLoS One 2014;9:e114373.
    • (2014) PLoS One , vol.9
    • Singh, A.K.1    Menendez-Conejero, R.2    San Martin, C.3    van Raaij, M.J.4
  • 20
    • 0021092717 scopus 로고
    • Evidence for a repeating cross-beta sheet structure in the adenovirus fibre
    • Green NM, Wrigley NG, Russell WC, Martin SR, McLachlan AD. Evidence for a repeating cross-beta sheet structure in the adenovirus fibre. EMBO J 1983;2:1357–1365.
    • (1983) EMBO J , vol.2 , pp. 1357-1365
    • Green, N.M.1    Wrigley, N.G.2    Russell, W.C.3    Martin, S.R.4    McLachlan, A.D.5
  • 21
    • 0033613385 scopus 로고    scopus 로고
    • A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein
    • van Raaij MJ, Mitraki A, Lavigne G, Cusack S. A triple beta-spiral in the adenovirus fibre shaft reveals a new structural motif for a fibrous protein. Nature 1999;401:935–938.
    • (1999) Nature , vol.401 , pp. 935-938
    • van Raaij, M.J.1    Mitraki, A.2    Lavigne, G.3    Cusack, S.4
  • 22
    • 0028774724 scopus 로고
    • Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution
    • Xia D, Henry LJ, Gerard RD, Deisenhofer J. Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution. Structure 1994;2:1259–1270.
    • (1994) Structure , vol.2 , pp. 1259-1270
    • Xia, D.1    Henry, L.J.2    Gerard, R.D.3    Deisenhofer, J.4
  • 23
    • 23844542268 scopus 로고    scopus 로고
    • The influence of adenovirus fiber structure and function on vector development for gene therapy
    • Nicklin SA, Wu E, Nemerow GR, Baker AH. The influence of adenovirus fiber structure and function on vector development for gene therapy. Mol Ther 2005;12:384–393.
    • (2005) Mol Ther , vol.12 , pp. 384-393
    • Nicklin, S.A.1    Wu, E.2    Nemerow, G.R.3    Baker, A.H.4
  • 24
    • 85092098295 scopus 로고    scopus 로고
    • Family Adenoviridae. In Virus Taxonomy Classification and Nomenclature of Viruses. Ninth Report of the International Committee on Taxonomy of Viruses. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. San Diego Elsevier; 2012. p 125–141
    • Harrach B, Benko M, Both G, Brown M, Davison A, Echavarria M, Hess M, Jones M, Kajon A, Lehmkuhl H, Mautner V, Mittal S, Wadell G. Family Adenoviridae. In: Virus Taxonomy: Classification and Nomenclature of Viruses. Ninth Report of the International Committee on Taxonomy of Viruses. King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, editors. San Diego: Elsevier; 2012. p 125–141.
    • Harrach, B.1    Benko, M.2    Both, G.3    Brown, M.4    Davison, A.5    Echavarria, M.6    Hess, M.7    Jones, M.8    Kajon, A.9    Lehmkuhl, H.10    Mautner, V.11    Mittal, S.12    Wadell, G.13
  • 25
    • 0027352218 scopus 로고
    • Physicochemical properties and cytopathogenicity of an adenovirus-like agent isolated from corn snake (Elaphe guttata)
    • Juhasz A, Ahne W. Physicochemical properties and cytopathogenicity of an adenovirus-like agent isolated from corn snake (Elaphe guttata). Arch Virol 1993;130:429–439.
    • (1993) Arch Virol , vol.130 , pp. 429-439
    • Juhasz, A.1    Ahne, W.2
  • 27
    • 47749102165 scopus 로고    scopus 로고
    • Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus
    • Pantelic RS, Lockett LJ, Rothnagel R, Hankamer B, Both GW. Cryoelectron microscopy map of Atadenovirus reveals cross-genus structural differences from human adenovirus. J Virol 2008;82:7346–7356.
    • (2008) J Virol , vol.82 , pp. 7346-7356
    • Pantelic, R.S.1    Lockett, L.J.2    Rothnagel, R.3    Hankamer, B.4    Both, G.W.5
  • 28
    • 30044442097 scopus 로고    scopus 로고
    • Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses
    • Spinelli S, Desmyter A, Verrips CT, de Haard HJ, Moineau S, Cambillau C. Lactococcal bacteriophage p2 receptor-binding protein structure suggests a common ancestor gene with bacterial and mammalian viruses. Nat Struct Mol Biol 2006;13:85–89.
    • (2006) Nat Struct Mol Biol , vol.13 , pp. 85-89
    • Spinelli, S.1    Desmyter, A.2    Verrips, C.T.3    de Haard, H.J.4    Moineau, S.5    Cambillau, C.6
  • 29
    • 33744900391 scopus 로고    scopus 로고
    • Modular structure of the receptor binding proteins of Lactococcus lactis phages. The RBP structure of the temperate phage TP901-1
    • Spinelli S, Campanacci V, Blangy S, Moineau S, Tegoni M, Cambillau C. Modular structure of the receptor binding proteins of Lactococcus lactis phages. The RBP structure of the temperate phage TP901-1. J Biol Chem 2006;281:14256–14262.
    • (2006) J Biol Chem , vol.281 , pp. 14256-14262
    • Spinelli, S.1    Campanacci, V.2    Blangy, S.3    Moineau, S.4    Tegoni, M.5    Cambillau, C.6
  • 31
    • 3142729320 scopus 로고    scopus 로고
    • Crystal structure of species D adenovirus fiber knobs and their sialic acid binding sites
    • Burmeister WP, Guilligay D, Cusack S, Wadell G, Arnberg N. Crystal structure of species D adenovirus fiber knobs and their sialic acid binding sites. J Virol 2004;78:7727–7736.
    • (2004) J Virol , vol.78 , pp. 7727-7736
    • Burmeister, W.P.1    Guilligay, D.2    Cusack, S.3    Wadell, G.4    Arnberg, N.5
  • 32
    • 0028271931 scopus 로고
    • Bacterial biofilms and biofouling
    • Fletcher M. Bacterial biofilms and biofouling. Curr Opin Biotechnol 1994;5:302–306.
    • (1994) Curr Opin Biotechnol , vol.5 , pp. 302-306
    • Fletcher, M.1
  • 34
    • 0033591467 scopus 로고    scopus 로고
    • Bacterial biofilms: a common cause of persistent infections
    • Costerton JW, Stewart PS, Greenberg EP. Bacterial biofilms: a common cause of persistent infections. Science 1999;284:1318–1322.
    • (1999) Science , vol.284 , pp. 1318-1322
    • Costerton, J.W.1    Stewart, P.S.2    Greenberg, E.P.3
  • 35
    • 84883718302 scopus 로고    scopus 로고
    • Novel strategies for the prevention and treatment of biofilm related infections
    • Chen M, Yu Q, Sun H. Novel strategies for the prevention and treatment of biofilm related infections. Int J Mol Sci 2013;14:18488–18501.
    • (2013) Int J Mol Sci , vol.14 , pp. 18488-18501
    • Chen, M.1    Yu, Q.2    Sun, H.3
  • 36
    • 0000672670 scopus 로고
    • Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor
    • Catlin BW. Extracellular deoxyribonucleic acid of bacteria and a deoxyribonuclease inhibitor. Science 1956;124:441–442.
    • (1956) Science , vol.124 , pp. 441-442
    • Catlin, B.W.1
  • 37
    • 22244473009 scopus 로고    scopus 로고
    • The use of human deoxyribonuclease (rhDNase) in the management of cystic fibrosis
    • Suri R. The use of human deoxyribonuclease (rhDNase) in the management of cystic fibrosis. BioDrugs 2005;19:135–144.
    • (2005) BioDrugs , vol.19 , pp. 135-144
    • Suri, R.1
  • 39
    • 78650798814 scopus 로고    scopus 로고
    • Dispersal of biofilms by secreted, matrix degrading, bacterial DNase
    • Nijland R, Hall MJ, Burgess JG. Dispersal of biofilms by secreted, matrix degrading, bacterial DNase. PLoS One 2010;5:e15668.
    • (2010) PLoS One , vol.5
    • Nijland, R.1    Hall, M.J.2    Burgess, J.G.3
  • 40
    • 84929144039 scopus 로고    scopus 로고
    • MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins
    • Jones DT, Singh T, Kosciolek T, Tetchner S. MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins. Bioinformatics 2015;31:999–1006.
    • (2015) Bioinformatics , vol.31 , pp. 999-1006
    • Jones, D.T.1    Singh, T.2    Kosciolek, T.3    Tetchner, S.4
  • 44
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert M, Biegert A, Hauser A, Soding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat Methods 2012;9:173–175.
    • (2012) Nat Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 45
    • 0035018558 scopus 로고    scopus 로고
    • The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa
    • Nishijyo T, Haas D, Itoh Y. The CbrA-CbrB two-component regulatory system controls the utilization of multiple carbon and nitrogen sources in Pseudomonas aeruginosa. Mol Microbiol 2001;40:917–931.
    • (2001) Mol Microbiol , vol.40 , pp. 917-931
    • Nishijyo, T.1    Haas, D.2    Itoh, Y.3
  • 46
    • 79551494258 scopus 로고    scopus 로고
    • The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa
    • Yeung AT, Bains M, Hancock RE. The sensor kinase CbrA is a global regulator that modulates metabolism, virulence, and antibiotic resistance in Pseudomonas aeruginosa. J Bacteriol 2011;193:918–931.
    • (2011) J Bacteriol , vol.193 , pp. 918-931
    • Yeung, A.T.1    Bains, M.2    Hancock, R.E.3
  • 51
    • 25144506135 scopus 로고    scopus 로고
    • Viruses in the sea
    • Suttle CA. Viruses in the sea. Nature 2005;437:356–361.
    • (2005) Nature , vol.437 , pp. 356-361
    • Suttle, C.A.1
  • 52
    • 34548792911 scopus 로고    scopus 로고
    • Marine viruses–major players in the global ecosystem
    • Suttle CA. Marine viruses–major players in the global ecosystem. Nat Rev Microbiol 2007;5:801–812.
    • (2007) Nat Rev Microbiol , vol.5 , pp. 801-812
    • Suttle, C.A.1
  • 56
    • 2442589577 scopus 로고    scopus 로고
    • Type IV pilus structure and bacterial pathogenicity
    • Craig L, Pique ME, Tainer JA. Type IV pilus structure and bacterial pathogenicity. Nature Rev Microbiol 2004;2:363–378.
    • (2004) Nature Rev Microbiol , vol.2 , pp. 363-378
    • Craig, L.1    Pique, M.E.2    Tainer, J.A.3
  • 57
    • 0032568984 scopus 로고    scopus 로고
    • Type IV pili, transient bacterial aggregates, and virulence of enteropathogenic Escherichia coli
    • Bieber D, Ramer SW, Wu CY, Murray WJ, Tobe T, Fernandez R, Schoolnik GK. Type IV pili, transient bacterial aggregates, and virulence of enteropathogenic Escherichia coli. Science 1998;280:2114–2118.
    • (1998) Science , vol.280 , pp. 2114-2118
    • Bieber, D.1    Ramer, S.W.2    Wu, C.Y.3    Murray, W.J.4    Tobe, T.5    Fernandez, R.6    Schoolnik, G.K.7
  • 58
    • 77952241054 scopus 로고    scopus 로고
    • The Longus type IV pilus of enterotoxigenic Escherichia coli (ETEC) mediates bacterial self-aggregation and protection from antimicrobial agents
    • Clavijo AP, Bai J, Gomez-Duarte OG. The Longus type IV pilus of enterotoxigenic Escherichia coli (ETEC) mediates bacterial self-aggregation and protection from antimicrobial agents. Microb Pathog 2010;48:230–238.
    • (2010) Microb Pathog , vol.48 , pp. 230-238
    • Clavijo, A.P.1    Bai, J.2    Gomez-Duarte, O.G.3
  • 60
    • 72449198468 scopus 로고    scopus 로고
    • Distinctive profiles of infection and pathology in hamsters infected with Clostridium difficile strains 630 and B1
    • Goulding D, Thompson H, Emerson J, Fairweather NF, Dougan G, Douce GR. Distinctive profiles of infection and pathology in hamsters infected with Clostridium difficile strains 630 and B1. Infect Immun 2009;77:5478–5485.
    • (2009) Infect Immun , vol.77 , pp. 5478-5485
    • Goulding, D.1    Thompson, H.2    Emerson, J.3    Fairweather, N.F.4    Dougan, G.5    Douce, G.R.6
  • 61
    • 83755174215 scopus 로고    scopus 로고
    • Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria
    • Imam S, Chen Z, Roos DS, Pohlschroder M. Identification of surprisingly diverse type IV pili, across a broad range of gram-positive bacteria. PLoS One 2011;6:e28919.
    • (2011) PLoS One , vol.6
    • Imam, S.1    Chen, Z.2    Roos, D.S.3    Pohlschroder, M.4
  • 63
    • 84905702476 scopus 로고    scopus 로고
    • Identification, immunogenicity, and cross-reactivity of type IV pilin and pilin-like proteins from Clostridium difficile
    • Maldarelli GA, De Masi L, von Rosenvinge EC, Carter M, Donnenberg MS. Identification, immunogenicity, and cross-reactivity of type IV pilin and pilin-like proteins from Clostridium difficile. Pathog Dis 2014;71(3):302–14.
    • (2014) Pathog Dis , vol.71 , Issue.3 , pp. 302-314
    • Maldarelli, G.A.1    De Masi, L.2    von Rosenvinge, E.C.3    Carter, M.4    Donnenberg, M.S.5
  • 66
    • 37549005981 scopus 로고    scopus 로고
    • Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry
    • Li J, Lim MS, Li S, Brock M, Pique ME, Woods VL Jr., Craig L. Vibrio cholerae toxin-coregulated pilus structure analyzed by hydrogen/deuterium exchange mass spectrometry. Structure 2008;16:137–148.
    • (2008) Structure , vol.16 , pp. 137-148
    • Li, J.1    Lim, M.S.2    Li, S.3    Brock, M.4    Pique, M.E.5    Woods, V.L.6    Craig, L.7
  • 67
    • 84892957566 scopus 로고    scopus 로고
    • Evaluation of predictions in the CASP10 model refinement category
    • Nugent T, Cozzetto D, Jones DT. Evaluation of predictions in the CASP10 model refinement category. Proteins 2014; 82 (Suppl 2):98–111.
    • (2014) Proteins , vol.82 , pp. 98-111
    • Nugent, T.1    Cozzetto, D.2    Jones, D.T.3
  • 68
    • 84887364470 scopus 로고    scopus 로고
    • Advances in Rosetta structure prediction for difficult molecular-replacement problems
    • DiMaio F. Advances in Rosetta structure prediction for difficult molecular-replacement problems. Acta Crystallogr D Biol Crystallogr 2013;69:2202–2208.
    • (2013) Acta Crystallogr D Biol Crystallogr , vol.69 , pp. 2202-2208
    • DiMaio, F.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.