메뉴 건너뛰기




Volumn 857, Issue , 2012, Pages 107-136

Automated protein structure modeling with swiss-model workspace and the protein model portal

Author keywords

Automation; Comparative modeling; Homology modeling; Molecular models; Protein Model Portal; Protein structure prediction; QMEAN; Quality estimation; SWISS MODEL

Indexed keywords

PROTEIN;

EID: 84858126537     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-588-6_5     Document Type: Article
Times cited : (132)

References (112)
  • 2
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • DOI 10.1126/science.1065659
    • Baker, D. and A. Sali. (2001) Protein structure prediction and structural genomics. Science. 294, 93-96. (Pubitemid 32952955)
    • (2001) Science , vol.294 , Issue.5540 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 3
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • Sali, A. and T.L. Blundell. (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol. 234, 779-815. (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 4
    • 0001433241 scopus 로고
    • Knowledge based modelling of homologous proteins, part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
    • Sutcliffe, M.J., I. Haneef, D. Carney, and T.L. Blundell. (1987) Knowledge based modeling of homologous proteins, Part I: Threedimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377-384. (Pubitemid 18024012)
    • (1987) Protein Engineering , vol.1 , Issue.5 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 5
    • 0030053370 scopus 로고    scopus 로고
    • ProMod and Swiss-model: Internet-based tools for automated comparative protein modelling
    • Peitsch, M.C. (1996) ProMod and Swiss-Model: Internet-based tools for automated comparative protein modeling. Biochem Soc Trans. 24, 274-279. (Pubitemid 26052435)
    • (1996) Biochemical Society Transactions , vol.24 , Issue.1 , pp. 274-279
    • Peitsch, M.C.1
  • 6
    • 79952113376 scopus 로고    scopus 로고
    • Template-based protein structure modeling
    • Fiser, A. Template-based protein structure modeling. Methods Mol Biol. 673, 73-94.
    • Methods Mol Biol. , vol.673 , pp. 73-94
    • Fiser, A.1
  • 7
    • 20444484434 scopus 로고    scopus 로고
    • A decade of CASP: Progress, bottlenecks and prognosis in protein structure prediction
    • DOI 10.1016/j.sbi.2005.05.011, PII S0959440X05000953
    • Moult, J. (2005) A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol. 15, 285-289. (Pubitemid 40826447)
    • (2005) Current Opinion in Structural Biology , vol.15 , pp. 285-289
    • Moult, J.1
  • 8
    • 71749104018 scopus 로고    scopus 로고
    • Computational analysis of membrane proteins: The largest class of drug targets
    • Arinaminpathy, Y., E. Khurana, D.M. Engelman, and M.B. Gerstein. (2009) Computational analysis of membrane proteins: the largest class of drug targets. Drug Discov Today. 14, 1130-1135.
    • (2009) Drug Discov Today. , vol.14 , pp. 1130-1135
    • Arinaminpathy, Y.1    Khurana, E.2    Engelman, D.M.3    Gerstein, M.B.4
  • 9
    • 59849107733 scopus 로고    scopus 로고
    • Outcome of a workshop on applications of protein models in biomedical research
    • Schwede, T., A. Sali, B. Honig, M. Levitt, et al. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure. 17, 151-159.
    • (2009) Structure. , vol.17 , pp. 151-159
    • Schwede, T.1    Sali, A.2    Honig, B.3    Levitt, M.4
  • 10
    • 0036330267 scopus 로고    scopus 로고
    • About the use of protein models
    • Peitsch, M.C. (2002) About the use of protein models. Bioinformatics. 18, 934-938. (Pubitemid 34846475)
    • (2002) Bioinformatics , vol.18 , Issue.7 , pp. 934-938
    • Peitsch, M.C.1
  • 11
    • 84969257265 scopus 로고    scopus 로고
    • The biological applications of protein models
    • T. Schwede and M.C. Peitsch, Editors. 2008, World Scientifi c Publishing
    • Tramontano, A., The biological applications of protein models., in Computational Structural Biology, T. Schwede and M.C. Peitsch, Editors. 2008, World Scientifi c Publishing. p. 111-127.
    • Computational Structural Biology , pp. 111-127
    • Tramontano, A.1
  • 12
    • 33748300566 scopus 로고    scopus 로고
    • The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability
    • DOI 10.1091/mbc.E06-03-0200
    • Junne, T., T. Schwede, V. Goder, and M. Spiess. (2006) The plug domain of yeast Sec61p is important for effi cient protein translocation, but is not essential for cell viability. Mol Biol Cell. 17, 4063-4068. (Pubitemid 44330888)
    • (2006) Molecular Biology of the Cell , vol.17 , Issue.9 , pp. 4063-4068
    • Junne, T.1    Schwede, T.2    Goder, V.3    Spiess, M.4
  • 13
    • 71249140665 scopus 로고    scopus 로고
    • Protein structure prediction in structure-based ligand design and virtual screening
    • Grant, M.A. (2009) Protein structure prediction in structure-based ligand design and virtual screening. Comb Chem High Throughput Screen. 12, 940-960.
    • (2009) Comb Chem High Throughput Screen. , vol.12 , pp. 940-960
    • Grant, M.A.1
  • 15
    • 58849144738 scopus 로고    scopus 로고
    • Prospects for de novo phasing with de novo protein models
    • Das, R. and D. Baker. (2009) Prospects for de novo phasing with de novo protein models. Acta Crystallogr D Biol Crystallogr. 65, 169-175.
    • (2009) Acta Crystallogr D Biol Crystallogr. , vol.65 , pp. 169-175
    • Das, R.1    Baker, D.2
  • 16
    • 27544504227 scopus 로고    scopus 로고
    • Evaluating the usefulness of protein structure models for molecular replacement
    • DOI 10.1093/bioinformatics/bti1112
    • Giorgetti, A., D. Raimondo, A.E. Miele, and A. Tramontano. (2005) Evaluating the usefulness of protein structure models for molecular replacement. Bioinformatics. 21 Suppl 2, ii72-76. (Pubitemid 41535431)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Giorgetti, A.1    Raimondo, D.2    Miele, A.E.3    Tramontano, A.4
  • 17
    • 33645075435 scopus 로고    scopus 로고
    • Refi nement of protein structures by iterative comparative modeling and CryoEM density fi tting
    • Topf, M., M.L. Baker, M.A. Marti-Renom, W. Chiu, et al. (2006) Refi nement of protein structures by iterative comparative modeling and CryoEM density fi tting. J Mol Biol. 357, 1655-1668.
    • (2006) J Mol Biol. , vol.357 , pp. 1655-1668
    • Topf, M.1    Baker, M.L.2    Marti-Renom, M.A.3    Chiu, W.4
  • 18
    • 25844459522 scopus 로고    scopus 로고
    • Combining electron microscopy and comparative protein structure modeling
    • DOI 10.1016/j.sbi.2005.08.001, PII S0959440X05001491, Carbohydrates and Glycoconjugates/Biophysical Methods
    • Topf, M. and A. Sali. (2005) Combining electron microscopy and comparative protein structure modeling. Curr Opin Struct Biol. 15, 578-585. (Pubitemid 41393490)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.5 , pp. 578-585
    • Topf, M.1    Sali, A.2
  • 19
    • 77649336168 scopus 로고    scopus 로고
    • Building and refi ning protein models within on homology modeling and multiscale structure refi nement
    • Zhu, J., L. Cheng, Q. Fang, Z.H. Zhou, et al. Building and refi ning protein models within on homology modeling and multiscale structure refi nement. J Mol Biol. 397, 835-851.
    • J Mol Biol. , vol.397 , pp. 835-851
    • Zhu, J.1    Cheng, L.2    Fang, Q.3    Zhou, Z.H.4
  • 20
    • 69249212321 scopus 로고    scopus 로고
    • Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
    • Guex, N., M.C. Peitsch, and T. Schwede. (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis. 30 Suppl 1, S162-173.
    • (2009) Electrophoresis. , vol.30 , Issue.SUPPL. 1
    • Guex, N.1    Peitsch, M.C.2    Schwede, T.3
  • 21
    • 77954262660 scopus 로고    scopus 로고
    • Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory
    • Brazas, M.D., J.T. Yamada, and B.F. Ouellette. (2010) Providing web servers and training in Bioinformatics: 2010 update on the Bioinformatics Links Directory. Nucleic Acids Res. 38 Suppl, W3-6.
    • (2010) Nucleic Acids Res. , vol.38 , Issue.SUPPL.
    • Brazas, M.D.1    Yamada, J.T.2    Ouellette, B.F.3
  • 23
    • 78651290702 scopus 로고    scopus 로고
    • ModBase, a database of annotated comparative protein structure models, and associated resources
    • Pieper, U., B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 39, D465-474.
    • (2011) Nucleic Acids Res. , vol.39
    • Pieper, U.1    Webb, B.M.2    Barkan, D.T.3    Schneidman-Duhovny, D.4
  • 24
    • 33750210515 scopus 로고    scopus 로고
    • Homology modeling using parametric alignment ensemble generation with consensus and energybased model selection
    • Chivian, D. and D. Baker. (2006) Homology modeling using parametric alignment ensemble generation with consensus and energybased model selection. Nucleic Acids Res. 34, e112.
    • (2006) Nucleic Acids Res. , vol.34
    • Chivian, D.1    Baker, D.2
  • 25
    • 74249104499 scopus 로고    scopus 로고
    • Fast and accurate automatic structure prediction with HHpred
    • Hildebrand, A., M. Remmert, A. Biegert, and J. Soding. (2009) Fast and accurate automatic structure prediction with HHpred. Proteins. 77 Suppl 9, 128-132.
    • (2009) Proteins. , vol.77 , Issue.SUPPL. 9 , pp. 128-132
    • Hildebrand, A.1    Remmert, M.2    Biegert, A.3    Soding, J.4
  • 26
    • 39449115394 scopus 로고    scopus 로고
    • I-TASSER server for protein 3D structure prediction
    • Zhang, Y. (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 9, 40.
    • (2008) BMC Bioinformatics. , vol.9 , pp. 40
    • Zhang, Y.1
  • 27
    • 79551598303 scopus 로고    scopus 로고
    • Improved predictions by pcons.net using multiple templates
    • Larsson, P., M.J. Skwark, B. Wallner, and A. Elofsson. Improved predictions by Pcons.net using multiple templates. Bioinformatics. 27, 426-427.
    • Bioinformatics , vol.27 A , pp. 426-427
    • Larsson, P.1    Skwark, M.J.2    Wallner, B.3    Elofsson, A.4
  • 28
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the Web: A case study using the Phyre server
    • Kelley, L.A. and M.J. Sternberg. (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc. 4, 363-371.
    • (2009) Nat Protoc. , vol.4 , pp. 363-371
    • Kelley, L.A.1    Sternberg, M.J.2
  • 30
    • 79851511415 scopus 로고    scopus 로고
    • Macromolecular docking restrained by a small angle X-ray scattering profile
    • Schneidman-Duhovny, D., M. Hammel, and A. Sali. (2011) Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol 173, 461-471.
    • (2011) J Struct Biol , vol.173 , pp. 461-471
    • Schneidman-Duhovny, D.1    Hammel, M.2    Sali, A.3
  • 32
    • 33645793799 scopus 로고    scopus 로고
    • Structure modeling of all identifi ed G protein-coupled receptors in the human genome
    • Zhang, Y., M.E. Devries, and J. Skolnick. (2006) Structure modeling of all identifi ed G protein-coupled receptors in the human genome. PLoS Comput Biol. 2, e13.
    • (2006) PLoS Comput Biol. , vol.2
    • Zhang, Y.1    Devries, M.E.2    Skolnick, J.3
  • 33
    • 50549090182 scopus 로고    scopus 로고
    • PIGS: Automatic prediction of antibody structures
    • Marcatili, P., A. Rosi, and A. Tramontano. (2008) PIGS: automatic prediction of antibody structures. Bioinformatics. 24, 1953-1954.
    • (2008) Bioinformatics. , vol.24 , pp. 1953-1954
    • Marcatili, P.1    Rosi, A.2    Tramontano, A.3
  • 34
    • 59449096415 scopus 로고    scopus 로고
    • Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking
    • Sivasubramanian, A., A. Sircar, S. Chaudhury, and J.J. Gray. (2009) Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking. Proteins. 74, 497-514.
    • (2009) Proteins. , vol.74 , pp. 497-514
    • Sivasubramanian, A.1    Sircar, A.2    Chaudhury, S.3    Gray, J.J.4
  • 35
    • 0034096904 scopus 로고    scopus 로고
    • Protein structure computing in the genomic era
    • DOI 10.1016/S0923-2508(00)00121-2
    • Schwede, T., A. Diemand, N. Guex, and M.C. Peitsch. (2000) Protein structure computing in the genomic era. Res Microbiol. 151, 107-112. (Pubitemid 30366696)
    • (2000) Research in Microbiology , vol.151 , Issue.2 , pp. 107-112
    • Schwede, T.1    Diemand, A.2    Guex, N.3    Peitsch, M.C.4
  • 37
    • 78651290702 scopus 로고    scopus 로고
    • ModBase, a database of annotated comparative protein structure models, and associated resources
    • Pieper, U., B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res 39, D465-D474.
    • (2011) Nucleic Acids Res , vol.39
    • Pieper, U.1    Webb, B.M.2    Barkan, D.T.3    Schneidman-Duhovny, D.4
  • 39
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia, C. and A.M. Lesk. (1986) The relation between the divergence of sequence and structure in proteins. Embo J. 5, 823-826.
    • (1986) Embo J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lesk, A.M.2
  • 40
    • 77954196482 scopus 로고    scopus 로고
    • Low-homology protein threading
    • Peng, J. and J. Xu. (2010) Low-homology protein threading. Bioinformatics. 26, i294-300.
    • (2010) Bioinformatics. , vol.26
    • Peng, J.1    Xu, J.2
  • 41
    • 74249088516 scopus 로고    scopus 로고
    • Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
    • Benkert, P., S.C. Tosatto, and T. Schwede. (2009) Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins. 77 Suppl 9, 173-180.
    • (2009) Proteins. , vol.77 , Issue.SUPPL. 9 , pp. 173-180
    • Benkert, P.1    Tosatto, S.C.2    Schwede, T.3
  • 42
    • 77950478720 scopus 로고    scopus 로고
    • Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments
    • McGuffi n, L.J. and D.B. Roche. (2010) Rapid model quality assessment for protein structure predictions using the comparison of multiple models without structural alignments. Bioinformatics. 26, 182-188.
    • (2010) Bioinformatics. , vol.26 , pp. 182-188
    • McGuffi, N.L.J.1    Roche, D.B.2
  • 43
    • 55549141879 scopus 로고    scopus 로고
    • How well can the accuracy of comparative protein structure models be predicted?
    • Eramian, D., N. Eswar, M.Y. Shen, and A. Sali. (2008) How well can the accuracy of comparative protein structure models be predicted? Protein Sci. 17, 1881-1893.
    • (2008) Protein Sci. , vol.17 , pp. 1881-1893
    • Eramian, D.1    Eswar, N.2    Shen, M.Y.3    Sali, A.4
  • 45
    • 0036838311 scopus 로고    scopus 로고
    • Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
    • DOI 10.1110/ps.0217002
    • Zhou, H. and Y. Zhou. (2002) Distancescaled, fi nite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11, 2714-2726. (Pubitemid 35191145)
    • (2002) Protein Science , vol.11 , Issue.11 , pp. 2714-2726
    • Zhou, H.1    Zhou, Y.2
  • 46
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • DOI 10.1002/elps.1150181505
    • Guex, N. and M.C. Peitsch. (1997) SWISSMODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis. 18, 2714-2723. (Pubitemid 28059943)
    • (1997) Electrophoresis , vol.18 , Issue.15 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 47
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • DOI 10.1093/bioinformatics/bti770
    • Arnold, K., L. Bordoli, J. Kopp, and T. Schwede. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modeling. Bioinformatics. 22, 195-201. (Pubitemid 43205406)
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 49
    • 0029004590 scopus 로고
    • Protein modeling by E-Mail
    • Peitsch, M.C. (1995) Protein modeling by E-Mail. BioTechnology. 13, 658-660.
    • (1995) BioTechnology. , vol.13 , pp. 658-660
    • Peitsch, M.C.1
  • 51
    • 67650358909 scopus 로고    scopus 로고
    • QMEAN server for protein model quality estimation
    • Benkert, P., M. Kunzli, and T. Schwede. (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res. 37, W510-514.
    • (2009) Nucleic Acids Res. , vol.37
    • Benkert, P.1    Kunzli, M.2    Schwede, T.3
  • 53
    • 58149204068 scopus 로고    scopus 로고
    • The protein structure initiative structural genomics knowledgebase
    • Berman, H.M., J.D. Westbrook, M.J. Gabanyi, W. Tao, et al. (2009) The protein structure initiative structural genomics knowledgebase. Nucleic Acids Res. 37, D365-368.
    • (2009) Nucleic Acids Res. , vol.37
    • Berman, H.M.1    Westbrook, J.D.2    Gabanyi, M.J.3    Tao, W.4
  • 54
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • DOI 10.1093/nar/gkl971
    • Berman, H., K. Henrick, H. Nakamura, and J.L. Markley. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res. 35, D301-303. (Pubitemid 46056219)
    • (2007) Nucleic Acids Research , vol.35 , Issue.SUPPL. 1
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 55
    • 78651290702 scopus 로고    scopus 로고
    • ModBase, a database of annotated comparative protein structure models, and associated resources
    • Pieper, U., B.M. Webb, D.T. Barkan, D. Schneidman-Duhovny, et al. (2011) ModBase, a database of annotated comparative protein structure models, and associated resources. Nucleic Acids Res. 56, D465-474.
    • (2011) Nat Protoc , vol.56
    • Pieper, U.1    Webb, B.M.2    Barkan, D.T.3    Schneidman-Duhovny, D.4
  • 56
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unifi ed platform for automated protein structure and function prediction
    • Roy, A., A. Kucukural, and Y. Zhang. (2010) I-TASSER: a unifi ed platform for automated protein structure and function prediction. Nat Protoc. 5, 725-738.
    • (2010) Nucleic Acids Res. , vol.5 , pp. 725-738
    • Roy, A.1    Kucukural, A.2    Zhang, Y.3
  • 57
    • 0038386050 scopus 로고    scopus 로고
    • 3D-Jury: A simple approach to improve protein structure predictions
    • DOI 10.1093/bioinformatics/btg124
    • Ginalski, K., A. Elofsson, D. Fischer, and L. Rychlewski. (2003) 3D-Jury: a simple approach to improve protein structure predictions. Bioinformatics. 19, 1015-1018. (Pubitemid 36675823)
    • (2003) Bioinformatics , vol.19 , Issue.8 , pp. 1015-1018
    • Ginalski, K.1    Elofsson, A.2    Fischer, D.3    Rychlewski, L.4
  • 58
    • 39149099199 scopus 로고    scopus 로고
    • The ModFOLD server for the quality assessment of protein structural models
    • McGuffi n, L.J. (2008) The ModFOLD server for the quality assessment of protein structural models. Bioinformatics. 24, 586-587.
    • (2008) Bioinformatics. , vol.24 , pp. 586-587
    • McGuffin, L.J.1
  • 59
    • 0038820376 scopus 로고    scopus 로고
    • Astex Viewer™: A visualisation aid for structure-based drug design
    • DOI 10.1023/A:1023813504011
    • Hartshorn, M.J. (2002) AstexViewer: a visualisation aid for structure-based drug design. J Comput Aided Mol Des. 16, 871-881. (Pubitemid 36701523)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.12 , pp. 871-881
    • Hartshorn, M.J.1
  • 60
    • 36549003965 scopus 로고    scopus 로고
    • InterPro and InterProScan: Tools for protein sequence classification and comparison
    • DOI 10.1385/1-59745-515-6:59, Comparative Genomics
    • Mulder, N. and R. Apweiler. (2007) InterPro and InterProScan: tools for protein sequence classifi cation and comparison. Methods Mol Biol. 396, 59-70. (Pubitemid 350190034)
    • (2007) Methods in Molecular Biology , vol.396 , pp. 59-70
    • Mulder, N.1    Apweiler, R.2
  • 61
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • DOI 10.1006/jmbi.1999.3091
    • Jones, D.T. (1999) Protein secondary structure prediction based on position-specifi c scoring matrices. J Mol Biol. 292, 195-202. (Pubitemid 29435759)
    • (1999) Journal of Molecular Biology , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 62
    • 0242362157 scopus 로고    scopus 로고
    • Prediction of disordered regions in proteins from position specific score matrices
    • DOI 10.1002/prot.10528
    • Jones, D.T. and J.J. Ward. (2003) Prediction of disordered regions in proteins from position specifi c score matrices. Proteins. 53 Suppl 6, 573-578. (Pubitemid 37352218)
    • (2003) Proteins: Structure, Function and Genetics , vol.53 , Issue.SUPPL. 6 , pp. 573-578
    • Jones, D.T.1    Ward, J.J.2
  • 63
    • 34047151404 scopus 로고    scopus 로고
    • Improving the accuracy of transmembrane protein topology prediction using evolutionary information
    • DOI 10.1093/bioinformatics/btl677
    • Jones, D.T. (2007) Improving the accuracy of transmembrane protein topology prediction using evolutionary information. Bioinformatics. 23, 538-544. (Pubitemid 46522586)
    • (2007) Bioinformatics , vol.23 , Issue.5 , pp. 538-544
    • Jones, D.T.1
  • 65
    • 16344373015 scopus 로고    scopus 로고
    • Protein homology detection by HMM-HMM comparison
    • DOI 10.1093/bioinformatics/bti125
    • Soding, J. (2005) Protein homology detection by HMM-HMM comparison. Bioinformatics. 21, 951-960. (Pubitemid 40467915)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 951-960
    • Soding, J.1
  • 67
    • 0000243829 scopus 로고
    • PROCHECK: A program to check the stereochemical quality of protein structures
    • Laskowski, R.A., M.W. MacArthur, D.S. Moss, and J.M. Thornton. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst. 26, 283-291.
    • (1993) J Appl Cryst. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 68
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. and C. Sander. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22, 2577-2637.
    • (1983) Biopolymers. , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 69
    • 0030039296 scopus 로고    scopus 로고
    • PROMOTIF - A program to identify and analyze structural motifs in proteins
    • Hutchinson, E.G. and J.M. Thornton. (1996) PROMOTIF-a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212-220. (Pubitemid 26054277)
    • (1996) Protein Science , vol.5 , Issue.2 , pp. 212-220
    • Hutchinson, E.G.1    Thornton, J.M.2
  • 71
    • 62949125048 scopus 로고    scopus 로고
    • 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins
    • Stroud, R.M., S. Choe, J. Holton, H.R. Kaback, et al. (2009) 2007 annual progress report synopsis of the Center for Structures of Membrane Proteins. J Struct Funct Genomics. 10, 193-208.
    • (2009) J Struct Funct Genomics. , vol.10 , pp. 193-208
    • Stroud, R.M.1    Choe, S.2    Holton, J.3    Kaback, H.R.4
  • 74
    • 77956187416 scopus 로고    scopus 로고
    • The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium
    • Xiao, R., S. Anderson, J. Aramini, R. Belote, et al. (2010) The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol. 172, 21-33.
    • (2010) J Struct Biol. , vol.172 , pp. 21-33
    • Xiao, R.1    Anderson, S.2    Aramini, J.3    Belote, R.4
  • 76
    • 84858118101 scopus 로고    scopus 로고
    • http://jcmm.burnham.org/.
  • 78
    • 0037346498 scopus 로고    scopus 로고
    • Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus
    • DOI 10.1046/j.1365-2958.2003.03401.x
    • Aldridge, P., R. Paul, P. Goymer, P. Rainey, et al. (2003) Role of the GGDEF regulator PleD in polar development of Caulobacter crescentus. Mol Microbiol. 47, 1695-1708. (Pubitemid 36363349)
    • (2003) Molecular Microbiology , vol.47 , Issue.6 , pp. 1695-1708
    • Aldridge, P.1    Paul, R.2    Goymer, P.3    Rainey, P.4    Jenal, U.5
  • 79
    • 33845403359 scopus 로고    scopus 로고
    • Mechanisms of cyclic-di-GMP signaling in bacteria
    • DOI 10.1146/annurev.genet.40.110405.090423
    • Jenal, U. and J. Malone. (2006) Mechanisms of cyclic-di-GMP signaling in bacteria. Annu Rev Genet. 40, 385-407. (Pubitemid 44956791)
    • (2006) Annual Review of Genetics , vol.40 , pp. 385-407
    • Jenal, U.1    Malone, J.2
  • 80
    • 33644873213 scopus 로고    scopus 로고
    • The Universal Protein Resource (UniProt): An expanding universe of protein information
    • Wu, C.H., R. Apweiler, A. Bairoch, D.A. Natale, et al. (2006) The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res. 34, D187-191.
    • (2006) Nucleic Acids Res. , vol.34
    • Wu, C.H.1    Apweiler, R.2    Bairoch, A.3    Natale, D.A.4
  • 83
    • 34547659282 scopus 로고    scopus 로고
    • --modified response regulator PleD: Implications for diguanylate cyclase activation, catalysis, and feedback inhibition
    • DOI 10.1016/j.str.2007.06.016, PII S0969212607002493
    • Wassmann, P., C. Chan, R. Paul, A. Beck, et al. (2007) Structure of BeF3-modifi ed response regulator PleD: implications for diguanylate cyclase activation, catalysis, and feedback inhibition. Structure. 15, 915-927. (Pubitemid 47212753)
    • (2007) Structure , vol.15 , Issue.8 , pp. 915-927
    • Wassmann, P.1    Chan, C.2    Paul, R.3    Beck, A.4    Heerklotz, H.5    Jenal, U.6    Schirmer, T.7
  • 84
    • 41749103519 scopus 로고    scopus 로고
    • Phosphorylation-independent regulation of the diguanylate cyclase WspR
    • De, N., M. Pirruccello, P.V. Krasteva, N. Bae, et al. (2008) Phosphorylation-independent regulation of the diguanylate cyclase WspR. PLoS Biol. 6, e67.
    • (2008) PLoS Biol. , vol.6
    • De, N.1    Pirruccello, M.2    Krasteva, P.V.3    Bae, N.4
  • 86
    • 33744779891 scopus 로고    scopus 로고
    • Sequence comparison and protein structure prediction
    • DOI 10.1016/j.sbi.2006.05.006, PII S0959440X06000789
    • Dunbrack, R.L., Jr. (2006) Sequence comparison and protein structure prediction. Curr Opin Struct Biol. 16, 374-384. (Pubitemid 43831651)
    • (2006) Current Opinion in Structural Biology , vol.16 , Issue.3 , pp. 374-384
    • Dunbrack Jr., R.L.1
  • 87
    • 65449188232 scopus 로고    scopus 로고
    • Jalview Version 2-a multiple sequence alignment editor and analysis workbench
    • Waterhouse, A.M., J.B. Procter, D.M. Martin, M. Clamp, et al. (2009) Jalview Version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics. 25, 1189-1191.
    • (2009) Bioinformatics. , vol.25 , pp. 1189-1191
    • Waterhouse, A.M.1    Procter, J.B.2    Martin, D.M.3    Clamp, M.4
  • 88
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. (1999) Twilight zone of protein sequence alignments. Protein Eng. 12, 85-94. (Pubitemid 29103686)
    • (1999) Protein Engineering , vol.12 , Issue.2 , pp. 85-94
    • Rost, B.1
  • 89
    • 34548232365 scopus 로고    scopus 로고
    • Inference of macromolecular assemblies from crystalline state
    • DOI 10.1016/j.jmb.2007.05.022, PII S0022283607006420
    • Krissinel, E. and K. Henrick. (2007) Inference of macromolecular assemblies from crystalline state. J Mol Biol. 372, 774-797. (Pubitemid 47321791)
    • (2007) Journal of Molecular Biology , vol.372 , Issue.3 , pp. 774-797
    • Krissinel, E.1    Henrick, K.2
  • 90
    • 35748950123 scopus 로고    scopus 로고
    • Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization
    • DOI 10.1074/jbc.M704702200
    • Paul, R., S. Abel, P. Wassmann, A. Beck, et al. (2007) Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J Biol Chem. 282, 29170-29177. (Pubitemid 350043379)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.40 , pp. 29170-29177
    • Paul, R.1    Abel, S.2    Wassmann, P.3    Beck, A.4    Heerklotz, H.5    Jenal, U.6
  • 91
    • 35748950123 scopus 로고    scopus 로고
    • Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization
    • DOI 10.1074/jbc.M704702200
    • Paul, R., S. Abel, P. Wassmann, A. Beck, et al. (2007) Activation of the diguanylate cyclase PleD by phosphorylation-mediated dimerization. J Biol Chem. 282, 29170-29177. (Pubitemid 350043379)
    • (2007) Journal of Biological Chemistry , vol.282 , Issue.40 , pp. 29170-29177
    • Paul, R.1    Abel, S.2    Wassmann, P.3    Beck, A.4    Heerklotz, H.5    Jenal, U.6
  • 92
    • 79551613290 scopus 로고    scopus 로고
    • Toward the estimation of the absolute quality of individual protein structure models
    • Benkert, P., M. Biasini, and T. Schwede. (2011) Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics. 27, 343-350.
    • (2011) Bioinformatics. , vol.27 , pp. 343-350
    • Benkert, P.1    Biasini, M.2    Schwede, T.3
  • 94
    • 0028346737 scopus 로고
    • Interferon α selectively affects expression of the human myeloid cell nuclear differentiation antigen in late stage cells in the monocytic but not the granulocytic lineage
    • Briggs, R., L. Dworkin, J. Briggs, E. Dessypris, et al. (1994) Interferon alpha selectively affects expression of the human myeloid cell nuclear differentiation antigen in late stage cells in the monocytic but not the granulocytic lineage. J Cell Biochem. 54, 198-206. (Pubitemid 24081049)
    • (1994) Journal of Cellular Biochemistry , vol.54 , Issue.2 , pp. 198-206
    • Briggs, R.1    Dworkin, L.2    Briggs, J.3    Dessypris, E.4    Stein, J.5    Stein, G.6    Lian, J.7
  • 95
    • 0028268918 scopus 로고
    • The human myeloid cell nuclear differentiation antigen gene is one of at least two related interferon-inducible genes located on chromosome 1q that are expressed specifically in hematopoietic cells
    • Briggs, R.C., J.A. Briggs, J. Ozer, L. Sealy, et al. (1994) The human myeloid cell nuclear differentiation antigen gene is one of at least two related interferon-inducible genes located on chromosome 1q that are expressed specifi-cally in hematopoietic cells. Blood. 83, 2153-2162. (Pubitemid 24112726)
    • (1994) Blood , vol.83 , Issue.8 , pp. 2153-2162
    • Briggs, R.C.1    Briggs, J.A.2    Ozer, J.3    Sealy, L.4    Dworkin, L.L.5    Kingsmore, S.F.6    Seldin, M.F.7    Kaur, G.P.8    Athwal, R.S.9    Dessypris, E.N.10
  • 96
    • 0028908735 scopus 로고
    • The closely linked genes encoding the myeloid nuclear differentiation antigen (MNDA) and IFI16 exhibit contrasting haemopoietic expression
    • DOI 10.1007/BF00188431
    • Dawson, M.J., J.A. Trapani, R.C. Briggs, J.K. Nicholl, et al. (1995) The closely linked genes encoding the myeloid nuclear differentiation antigen (MNDA) and IFI16 exhibit contrasting haemopoietic expression. Immunogenetics. 41, 40-43. (Pubitemid 24373338)
    • (1995) Immunogenetics , vol.41 , Issue.1 , pp. 40-43
    • Dawson, M.J.1    Trapani, J.A.2    Briggs, R.C.3    Nicholl, J.K.4    Sutherland, G.R.5    Baker, E.6
  • 97
    • 58149178579 scopus 로고    scopus 로고
    • NCBI Reference Sequences: Current status, policy and new initiatives
    • Pruitt, K.D., T. Tatusova, W. Klimke, and D.R. Maglott. (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res. 37, D32-36.
    • (2009) Nucleic Acids Res. , vol.37
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 98
    • 3042818018 scopus 로고    scopus 로고
    • The international protein index: An integrated database for proteomics experiments
    • DOI 10.1002/pmic.200300721
    • Kersey, P.J., J. Duarte, A. Williams, Y. Karavidopoulou, et al. (2004) The International Protein Index: an integrated database for proteomics experiments. Proteomics. 4, 1985-1988. (Pubitemid 38880363)
    • (2004) Proteomics , vol.4 , Issue.7 , pp. 1985-1988
    • Kersey, P.J.1    Duarte, J.2    Williams, A.3    Karavidopoulou, Y.4    Birney, E.5    Apweiler, R.6
  • 100
    • 33750460983 scopus 로고    scopus 로고
    • Searching NCBI databases using Entrez
    • Chapter 1, Unit 1 3
    • Baxevanis, A.D. (2008) Searching NCBI databases using Entrez. Curr Protoc Bioinformatics. Chapter 1, Unit 1 3.
    • (2008) Curr Protoc Bioinformatics
    • Baxevanis, A.D.1
  • 101
    • 8844222708 scopus 로고    scopus 로고
    • TargetDB: A target registration database for structural genomics projects
    • DOI 10.1093/bioinformatics/bth300
    • Chen, L., R. Oughtred, H.M. Berman, and J. Westbrook. (2004) TargetDB: a target registration database for structural genomics projects. Bioinformatics. 20, 2860-2862. (Pubitemid 39530181)
    • (2004) Bioinformatics , vol.20 , Issue.16 , pp. 2860-2862
    • Chen, L.1    Oughtred, R.2    Berman, H.M.3    Westbrook, J.4
  • 102
    • 84858118099 scopus 로고    scopus 로고
    • Saito, K., M. Inoue, S. Koshiba, T. Kigawa, et al. (2006) DOI: 10.2210/pdb2dbg/pdb
    • Saito, K., M. Inoue, S. Koshiba, T. Kigawa, et al. (2006) DOI: 10.2210/pdb2dbg/pdb.
  • 104
    • 84858118098 scopus 로고    scopus 로고
    • http://www.nesg.org/.
  • 107
    • 84858144648 scopus 로고    scopus 로고
    • Liao, J.C.C., R. Lam, M. Ravichandran, J. Ma, et al. (2007) DOI: 10.2210/pdb2oq0/ pdb
    • Liao, J.C.C., R. Lam, M. Ravichandran, J. Ma, et al. (2007) DOI: 10.2210/pdb2oq0/ pdb.
  • 108
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • DOI 10.1093/nar/gkg520
    • Schwede, T., J. Kopp, N. Guex, and M.C. Peitsch. (2003) SWISS-MODEL: An automated protein homology-modeling server. Nucleic Acids Res. 31, 3381-3385. (Pubitemid 37442164)
    • (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 109
    • 77957755921 scopus 로고    scopus 로고
    • The 2.2-Å structure of the HP0958 protein from Helicobacter pylori reveals a kinked anti-parallel coiled-coil hairpin domain and a highly conserved ZN-ribbon domain
    • Caly, D.L., P.W. O'Toole, and S.A. Moore. (2010) The 2.2-Å structure of the HP0958 protein from Helicobacter pylori reveals a kinked anti-parallel coiled-coil hairpin domain and a highly conserved ZN-ribbon domain. J Mol Biol. 403, 405-419.
    • (2010) J Mol Biol. , vol.403 , pp. 405-419
    • Caly, D.L.1    O'toole, P.W.2    Moore, S.A.3
  • 111
    • 84858145802 scopus 로고    scopus 로고
    • http://www. wwpdb. org/docs.html
    • http://blast.ncbi.nlm.nih.gov/ 112. http://www.wwpdb.org/docs.html.
  • 112
    • 61449229355 scopus 로고    scopus 로고
    • Protein structure homology modeling using SWISS-MODEL workspace
    • Bordoli, L., F. Kiefer, K. Arnold, P. Benkert, et al. (2009) Protein structure homology modeling using SWISS-MODEL workspace. Nat Protoc. 4, 1-13.
    • (2009) Nat Protoc. , vol.4 , pp. 1-13
    • Bordoli, L.1    Kiefer, F.2    Arnold, K.3    Benkert, P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.