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Volumn 42, Issue W1, 2014, Pages

SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; ENZYME ACTIVE SITE; HYDROPHOBICITY; MOLECULAR INTERACTION; ONLINE SYSTEM; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN DATA BANK; PROTEIN PURIFICATION; PROTEIN QUATERNARY STRUCTURE; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE HOMOLOGY; SWISS MODEL TEMPLATE LIBRARY; VALIDATION PROCESS; VAN DER WAALS INTERACTION; WEB BROWSER;

EID: 84904815625     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku340     Document Type: Article
Times cited : (4009)

References (35)
  • 1
    • 69249212321 scopus 로고    scopus 로고
    • Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: A historical perspective
    • Guex,N., Peitsch,M.C. and Schwede,T. (2009) Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective. Electrophoresis, 30(Suppl. 1), S162-S173.
    • (2009) Electrophoresis , vol.30 , Issue.SUPPL. 1
    • Guex, N.1    Peitsch, M.C.2    Schwede, T.3
  • 2
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede,T., Kopp,J., Guex,N. and Peitsch,M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 5
    • 32144432437 scopus 로고    scopus 로고
    • The SWISS-MODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold,K., Bordoli,L., Kopp,J. and Schwede,T. (2006) The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22, 195-201.
    • (2006) Bioinformatics , vol.22 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 6
    • 67650358909 scopus 로고    scopus 로고
    • QMEAN server for protein model quality estimation
    • Benkert,P., Kunzli,M. and Schwede,T. (2009) QMEAN server for protein model quality estimation. Nucleic Acids Res., 37, W510-W514.
    • (2009) Nucleic Acids Res. , vol.37
    • Benkert, P.1    Kunzli, M.2    Schwede, T.3
  • 7
    • 79551613290 scopus 로고    scopus 로고
    • Toward the estimation of the absolute quality of individual protein structure models
    • Benkert,P., Biasini,M. and Schwede,T. (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
  • 8
    • 84883481556 scopus 로고    scopus 로고
    • The protein model portal - A comprehensive resource for protein structure and model information
    • Haas,J., Roth,S., Arnold,K., Kiefer,F., Schmidt,T., Bordoli,L. and Schwede,T. (2013) The protein model portal-a comprehensive resource for protein structure and model information. Database (Oxford), 2013, bat031.
    • (2013) Database (Oxford) , vol.2013
    • Haas, J.1    Roth, S.2    Arnold, K.3    Kiefer, F.4    Schmidt, T.5    Bordoli, L.6    Schwede, T.7
  • 9
    • 33846036096 scopus 로고    scopus 로고
    • The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
    • Berman,H., Henrick,K., Nakamura,H. and Markley,J.L. (2007) The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 35, D301-D303.
    • (2007) Nucleic Acids Res. , vol.35
    • Berman, H.1    Henrick, K.2    Nakamura, H.3    Markley, J.L.4
  • 10
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali,A. and Blundell,T.L. (1993) Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 11
    • 84969256542 scopus 로고    scopus 로고
    • Protein structure modelling
    • Schwede,T. and Peitsch,M.C. (ed.). World Scientific Publishing, Singapore
    • Schwede,T., Sali,A., Eswar,N. and Peitsch,M.C. (2008) Protein Structure Modelling. In: Schwede,T. and Peitsch,M.C. (ed.). Computational Structural Biology. World Scientific Publishing, Singapore, pp. 3-35.
    • (2008) Computational Structural Biology , pp. 3-35
    • Schwede, T.1    Sali, A.2    Eswar, N.3    Peitsch, M.C.4
  • 13
    • 84856489442 scopus 로고    scopus 로고
    • HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment
    • Remmert,M., Biegert,A., Hauser,A. and Soding,J. (2012) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173-175.
    • (2012) Nat. Methods , vol.9 , pp. 173-175
    • Remmert, M.1    Biegert, A.2    Hauser, A.3    Soding, J.4
  • 14
    • 23144465987 scopus 로고    scopus 로고
    • SCRATCH: A protein structure and structural feature prediction server
    • Cheng,J., Randall,A.Z., Sweredoski,M.J. and Baldi,P. (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res., 33, W72-W76.
    • (2005) Nucleic Acids Res. , vol.33
    • Cheng, J.1    Randall, A.Z.2    Sweredoski, M.J.3    Baldi, P.4
  • 15
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones,D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
    • (1999) J. Mol. Biol. , vol.292 , pp. 195-202
    • Jones, D.T.1
  • 16
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch,W. and Sander,C. (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
  • 18
    • 35448938488 scopus 로고    scopus 로고
    • Benchmarking template selection and model quality assessment for high-resolution comparative modeling
    • Sadowski,M.I. and Jones,D.T. (2007) Benchmarking template selection and model quality assessment for high-resolution comparative modeling. Proteins, 69, 476-485.
    • (2007) Proteins , vol.69 , pp. 476-485
    • Sadowski, M.I.1    Jones, D.T.2
  • 19
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex,N. and Peitsch,M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18, 2714-2723.
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 20
    • 0035812694 scopus 로고    scopus 로고
    • Protein structure prediction and structural genomics
    • Baker,D. and Sali,A. (2001) Protein structure prediction and structural genomics. Science, 294, 93-96.
    • (2001) Science , vol.294 , pp. 93-96
    • Baker, D.1    Sali, A.2
  • 22
    • 77952770307 scopus 로고    scopus 로고
    • Analysis and prediction of protein quaternary structure
    • Poupon,A. and Janin,J. (2010) Analysis and prediction of protein quaternary structure. Methods Mol. Biol., 609, 349-364.
    • (2010) Methods Mol. Biol. , vol.609 , pp. 349-364
    • Poupon, A.1    Janin, J.2
  • 23
    • 80855132939 scopus 로고    scopus 로고
    • Assessment of template based protein structure predictions in CASP9
    • Mariani,V., Kiefer,F., Schmidt,T., Haas,J. and Schwede,T. (2011) Assessment of template based protein structure predictions in CASP9. Proteins, 79(Suppl. 10), 37-58.
    • (2011) Proteins , vol.79 , Issue.SUPPL. 10 , pp. 37-58
    • Mariani, V.1    Kiefer, F.2    Schmidt, T.3    Haas, J.4    Schwede, T.5
  • 24
    • 84871040640 scopus 로고    scopus 로고
    • CAD-score: A new contact area difference-based function for evaluation of protein structural models
    • Olechnovic,K., Kulberkyte,E. and Venclovas,C. (2013) CAD-score: a new contact area difference-based function for evaluation of protein structural models. Proteins, 81, 149-162.
    • (2013) Proteins , vol.81 , pp. 149-162
    • Olechnovic, K.1    Kulberkyte, E.2    Venclovas, C.3
  • 25
    • 84885990516 scopus 로고    scopus 로고
    • LDDT: A local superposition-free score for comparing protein structures and models using distance difference tests
    • Mariani,V., Biasini,M., Barbato,A. and Schwede,T. (2013) lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics, 29, 2722-2728.
    • (2013) Bioinformatics , vol.29 , pp. 2722-2728
    • Mariani, V.1    Biasini, M.2    Barbato, A.3    Schwede, T.4
  • 26
    • 84864448769 scopus 로고    scopus 로고
    • Template-based protein structure modeling using the RaptorX web server
    • Kallberg,M.,Wang,H., Wang,S., Peng,J., Wang,Z., Lu,H. and Xu,J. (2012) Template-based protein structure modeling using the RaptorX web server. Nat. Protoc., 7, 1511-1522.
    • (2012) Nat. Protoc. , vol.7 , pp. 1511-1522
    • Kallberg, M.1    Wang, H.2    Wang, S.3    Peng, J.4    Wang, Z.5    Lu, H.6    Xu, J.7
  • 27
    • 79960394811 scopus 로고    scopus 로고
    • Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates
    • Yang,Y., Faraggi,E., Zhao,H. and Zhou,Y. (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics, 27, 2076-2082.
    • (2011) Bioinformatics , vol.27 , pp. 2076-2082
    • Yang, Y.1    Faraggi, E.2    Zhao, H.3    Zhou, Y.4
  • 28
    • 63849246525 scopus 로고    scopus 로고
    • Protein structure prediction on the web: A case study using the Phyre server
    • Kelley,L.A. and Sternberg,M.J. (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
    • 84864125649 scopus 로고    scopus 로고
    • Improvement of 3D protein models using multiple templates guided by single-template model quality assessment
    • Buenavista,M.T., Roche,D.B. and McGuffin,L.J. (2012) Improvement of 3D protein models using multiple templates guided by single-template model quality assessment. Bioinformatics, 28, 1851-1857.
    • (2012) Bioinformatics , vol.28 , pp. 1851-1857
    • Buenavista, M.T.1    Roche, D.B.2    McGuffin, L.J.3
  • 31
    • 3242887695 scopus 로고    scopus 로고
    • Protein structure prediction and analysis using the Robetta server
    • Kim,D.E., Chivian,D. and Baker,D. (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res., 32, W526-W531.
    • (2004) Nucleic Acids Res. , vol.32
    • Kim, D.E.1    Chivian, D.2    Baker, D.3
  • 32
    • 23144452044 scopus 로고    scopus 로고
    • The HHpred interactive server for protein homology detection and structure prediction
    • Soding,J., Biegert,A. and Lupas,A.N. (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res., 33, W244-W248.
    • (2005) Nucleic Acids Res. , vol.33
    • Soding, J.1    Biegert, A.2    Lupas, A.N.3
  • 33
    • 78651319979 scopus 로고    scopus 로고
    • Ongoing and future developments at the universal protein resource
    • UniProt-Consortium
    • UniProt-Consortium. (2011) Ongoing and future developments at the universal protein resource. Nucleic Acids Res., 39, D214-D219.
    • (2011) Nucleic Acids Res. , vol.39
  • 34
    • 84903776217 scopus 로고    scopus 로고
    • Modelling three-dimensional protein structures for applications in drug design
    • doi:http://dx.doi.org/10.1016/j.drudis.2013.10.027
    • Schmidt,T., Bergner,A. and Schwede,T. (2013) Modelling three-dimensional protein structures for applications in drug design. Drug Discov. Today, doi:http://dx.doi.org/10.1016/j.drudis.2013.10.027.
    • (2013) Drug Discov. Today
    • Schmidt, T.1    Bergner, A.2    Schwede, T.3
  • 35
    • 84892964425 scopus 로고    scopus 로고
    • Assessment of the assessment: Evaluation of the model quality estimates in CASP10
    • Kryshtafovych,A., Barbato,A., Fidelis,K., Monastyrskyy,B., Schwede,T. and Tramontano,A. (2014) Assessment of the assessment: evaluation of the model quality estimates in CASP10. Proteins, 82(Suppl. 2), 112-126.
    • (2014) Proteins , vol.82 , Issue.SUPPL. 2 , pp. 112-126
    • Kryshtafovych, A.1    Barbato, A.2    Fidelis, K.3    Monastyrskyy, B.4    Schwede, T.5    Tramontano, A.6


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