Torsten Schwede

Summary

Affiliation: University of Basel
Country: Switzerland

Publications

  1. pmc OpenStructure: a flexible software framework for computational structural biology
    Marco Biasini
    Biozentrum, Universitat Basel, Basel, Switzerland
    Bioinformatics 26:2626-8. 2010
  2. pmc Toward the estimation of the absolute quality of individual protein structure models
    Pascal Benkert
    Biozentrum, University of Basel, Switzerland
    Bioinformatics 27:343-50. 2011
  3. pmc The SWISS-MODEL Repository and associated resources
    Florian Kiefer
    Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    Nucleic Acids Res 37:D387-92. 2009
  4. pmc The Protein Model Portal--a comprehensive resource for protein structure and model information
    Juergen Haas
    Biozentrum University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland
    Database (Oxford) 2013:bat031. 2013
  5. pmc The SWISS-MODEL Repository: new features and functionalities
    Jurgen Kopp
    Biozentrum der Universitat Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
    Nucleic Acids Res 34:D315-8. 2006
  6. pmc lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
    Valerio Mariani
    Biozentrum, Universitat Basel, Klingelbergstrasse 50 70 and Computational Structural Biology, SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
    Bioinformatics 29:2722-8. 2013
  7. pmc OpenStructure: an integrated software framework for computational structural biology
    M Biasini
    Biozentrum Universität Basel, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland
    Acta Crystallogr D Biol Crystallogr 69:701-9. 2013
  8. pmc Protein modeling: what happened to the "protein structure gap"?
    Torsten Schwede
    Biozentrum, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Electronic address
    Structure 21:1531-40. 2013
  9. pmc Outcome of a workshop on applications of protein models in biomedical research
    Torsten Schwede
    Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Structure 17:151-9. 2009
  10. pmc SWISS-MODEL: An automated protein homology-modeling server
    Torsten Schwede
    Biozentrum der Universitat Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 31:3381-5. 2003

Collaborators

Detail Information

Publications37

  1. pmc OpenStructure: a flexible software framework for computational structural biology
    Marco Biasini
    Biozentrum, Universitat Basel, Basel, Switzerland
    Bioinformatics 26:2626-8. 2010
    ..Several applications, such as the latest versions of IPLT and QMean, have been implemented based on OpenStructure-demonstrating its value for the development of next-generation structural biology algorithms...
  2. pmc Toward the estimation of the absolute quality of individual protein structure models
    Pascal Benkert
    Biozentrum, University of Basel, Switzerland
    Bioinformatics 27:343-50. 2011
    ..However, reliable absolute quality estimates are crucial to assess the suitability of a model for specific biomedical applications...
  3. pmc The SWISS-MODEL Repository and associated resources
    Florian Kiefer
    Biozentrum, University of Basel and SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    Nucleic Acids Res 37:D387-92. 2009
    ..proteinmodelportal.org) of the PSI Structural Genomics Knowledge Base facilitates the navigation between protein sequence and structure resources...
  4. pmc The Protein Model Portal--a comprehensive resource for protein structure and model information
    Juergen Haas
    Biozentrum University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland
    Database (Oxford) 2013:bat031. 2013
    ..The portal is updated regularly and actively developed to include latest methods in the field of computational structural biology. Database URL: http://www.proteinmodelportal.org...
  5. pmc The SWISS-MODEL Repository: new features and functionalities
    Jurgen Kopp
    Biozentrum der Universitat Basel and Swiss Institute of Bioinformatics, Basel, Switzerland
    Nucleic Acids Res 34:D315-8. 2006
    ..The SWISS-MODEL Repository is freely accessible at http://swissmodel.expasy.org/repository/...
  6. pmc lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests
    Valerio Mariani
    Biozentrum, Universitat Basel, Klingelbergstrasse 50 70 and Computational Structural Biology, SIB Swiss Institute of Bioinformatics, 4056 Basel, Switzerland
    Bioinformatics 29:2722-8. 2013
    ..Conventional similarity measures based on a global superposition of carbon α atoms are strongly influenced by domain motions and do not assess the accuracy of local atomic details in the model...
  7. pmc OpenStructure: an integrated software framework for computational structural biology
    M Biasini
    Biozentrum Universität Basel, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland
    Acta Crystallogr D Biol Crystallogr 69:701-9. 2013
    ..The framework has been released under the LGPL version 3 license and is available for download from http://www.openstructure.org...
  8. pmc Protein modeling: what happened to the "protein structure gap"?
    Torsten Schwede
    Biozentrum, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Computational Structural Biology, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, 4056 Basel, Switzerland Electronic address
    Structure 21:1531-40. 2013
    ....
  9. pmc Outcome of a workshop on applications of protein models in biomedical research
    Torsten Schwede
    Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Structure 17:151-9. 2009
    ....
  10. pmc SWISS-MODEL: An automated protein homology-modeling server
    Torsten Schwede
    Biozentrum der Universitat Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 31:3381-5. 2003
    ..The reliability of SWISS-MODEL is continuously evaluated in the EVA-CM project. The SWISS-MODEL server is under constant development to improve the successful implementation of expert knowledge into an easy-to-use server...
  11. pmc The Protein Model Portal
    Konstantin Arnold
    Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056, Basel, Switzerland
    J Struct Funct Genomics 10:1-8. 2009
    ..The PMP is available at http://www.proteinmodelportal.org and from the PSI Structural Genomics Knowledgebase...
  12. doi request reprint Assessment of template based protein structure predictions in CASP9
    Valerio Mariani
    Biozentrum University of Basel, Switzerland SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    Proteins 79:37-58. 2011
    ..Here, we present the results of our assessment of the CASP9 predictions in the category of template based modeling, documenting the state of the art and highlighting areas for future developments...
  13. doi request reprint Protein structure homology modeling using SWISS-MODEL workspace
    Lorenza Bordoli
    Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Nat Protoc 4:1-13. 2009
    ..However, this does not include the time required for visualization and interpretation of the model, which may vary depending on personal experience working with protein structures...
  14. doi request reprint Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer grid
    Michael Podvinec
    Swiss Institute of Bioinformatics and Biozentrum, University of Basel, Klingelbergstrasse 50, CH 4056 Basel, Switzerland
    J Med Chem 53:1483-95. 2010
    ..We discuss why this likely occurred for this particular target. We also describe our attempts to use aggregation prediction to further guide the study, following this finding...
  15. ncbi request reprint Assessment of disorder predictions in CASP7
    Lorenza Bordoli
    Biozentrum University of Basel, Basel, Switzerland
    Proteins 69:129-36. 2007
    ....
  16. ncbi request reprint Automated server predictions in CASP7
    James N D Battey
    Biozentrum, University of Basel, Basel, Switzerland
    Proteins 69:68-82. 2007
    ..This article summarizes the contribution of automated structure prediction servers in the CASP7 experiment, with emphasis on 3D structure prediction, as well as information on their prediction scope and public availability...
  17. doi request reprint Assessment of ligand-binding residue predictions in CASP9
    Tobias Schmidt
    Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, Basel, Switzerland
    Proteins 79:126-36. 2011
    ....
  18. doi request reprint Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspective
    Nicolas Guex
    Swiss Institute of Bioinformatics, Lausanne, Switzerland
    Electrophoresis 30:S162-73. 2009
    ..This has a very positive and enabling impact on many different applications in biomedical research as described in this paper...
  19. pmc QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density information
    Pascal Benkert
    Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50 70, 4056 Basel, Switzerland
    BMC Struct Biol 9:35. 2009
    ..In this paper we show that model selection can be improved if both approaches are combined by pre-filtering the models used during the calculation of the structural consensus...
  20. doi request reprint Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust
    Pascal Benkert
    Biozentrum, University of Basel, Basel 4056, Switzerland
    Proteins 77:173-80. 2009
    ..Both scoring functions are publicly available at http://swissmodel.expasy.org/qmean/...
  21. pmc QMEAN server for protein model quality estimation
    Pascal Benkert
    Biozentrum, University of Basel, Switzerland
    Nucleic Acids Res 37:W510-4. 2009
    ..The web server performs a ranking of the input models and highlights potentially problematic regions for each model. The QMEAN server is available at http://swissmodel.expasy.org/qmean...
  22. ncbi request reprint Assessment of CASP7 predictions for template-based modeling targets
    Jurgen Kopp
    Biozentrum, University of Basel, Switzerland
    Proteins 69:38-56. 2007
    ..Finally, we discuss some general conclusions about the state of the art of template-based modeling methods and their usefulness for practical applications...
  23. pmc The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models
    Jurgen Kopp
    Biozentrum der Universitat Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
    Nucleic Acids Res 32:D230-4. 2004
    ..The aim of the SWISS-MODEL Repository is to provide access to an up-to-date collection of annotated three-dimensional protein models generated by automated homology modelling, bridging the gap between sequence and structure databases...
  24. pmc Improving your target-template alignment with MODalign
    Alessandro Barbato
    Department of Physics, Sapienza University P le A Moro, 5, 00185 Rome, Italy
    Bioinformatics 28:1038-9. 2012
    ..Although it has been designed to simplify the target-template alignment step in modeling, it is suitable for all cases where a sequence alignment needs to be inspected in the context of other biological information...
  25. ncbi request reprint SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
    Marco Biasini
    Biozentrum, University of Basel, Basel 4056, Switzerland SIB Swiss Institute of Bioinformatics, Basel 4056, Switzerland
    Nucleic Acids Res 42:W252-8. 2014
    ..SWISS-MODEL is available at http://swissmodel.expasy.org/. ..
  26. ncbi request reprint How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding
    Holmfridur B Thorsteinsdottir
    Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
    Proteins 65:407-23. 2006
    ....
  27. ncbi request reprint Automated protein structure homology modeling: a progress report
    Jurgen Kopp
    Biozentrum der Universitat Basel and Swiss Institute of Bioinformatics, Klingelbergstr 50 70, CH 4056, Basel, Switzerland
    Pharmacogenomics 5:405-16. 2004
    ..Model repositories give access to these annotated and evaluated models. In this review, we will discuss recent developments in automated comparative modeling and provide selected examples illustrating the use of homology models...
  28. ncbi request reprint Computational analysis of methyl transfer reactions in dengue virus methyltransferase
    Tobias Schmidt
    Department of Chemistry, University of Basel, Klingelbergstrasse 80, 4056 Basel, Switzerland
    J Phys Chem B 118:5882-90. 2014
    ..One such compound in MeAzaSAM, an isostructural mimic of SAM, for which the present calculations suggest that the methyl transfer reaction is unlikely to occur under biologically relevant conditions. ..
  29. doi request reprint Assessment of ligand binding site predictions in CASP10
    Tiziano Gallo Cassarino
    Biozentrum, University of Basel, Basel, Switzerland SIB Swiss Institute of Bioinformatics, Basel, Switzerland
    Proteins 82:154-63. 2014
    ....
  30. doi request reprint Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal
    Lorenza Bordoli
    SIB Swiss Institute of Bioinformatics, Biozentrum University of Basel, Basel, Switzerland
    Methods Mol Biol 857:107-36. 2012
    ..In this chapter, we describe practical approaches for automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model Portal...
  31. ncbi request reprint Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity: a combined virtual screening and biological assay approach
    Marco Scarsi
    Biozentrum, University of Basel, Klingelbergstr 50 70, CH 4056 Basel, Switzerland
    Mol Pharmacol 71:398-406. 2007
    ..In addition, we provide a unified concept of the PPARgamma binding ability of seemingly disparate compound classes...
  32. pmc Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression
    Anna Duerig
    Biozentrum, University of Basel, 4056 Basel, Switzerland
    Genes Dev 23:93-104. 2009
    ..This is the first report that links cyclic di-GMP to protein dynamics and cell cycle control in bacteria...
  33. doi request reprint Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug design
    Narasimha Rao Uda
    University of Basel, Department of Chemistry, Spitalstrasse 51, Basel 4056, Switzerland
    Metallomics 6:88-95. 2014
    ..Moreover, to our knowledge, this is the first example of metallo-isoform heterogeneity in vivo that provides an evolutionary advantage to bacteria upon drug-challenge...
  34. ncbi request reprint The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Konstantin Arnold
    Biozentrum Basel, University of Basel Switzerland
    Bioinformatics 22:195-201. 2006
    ....
  35. ncbi request reprint Outcome of a workshop on archiving structural models of biological macromolecules
    Helen M Berman
    The Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, USA
    Structure 14:1211-7. 2006
  36. ncbi request reprint Domain definition and target classification for CASP7
    Neil D Clarke
    Genome Institute of Singapore, 138627 Singapore
    Proteins 69:10-8. 2007
    ..A total of 28 target domains from the template-based modeling category were also assessed in the high accuracy category and four overlapped with the free modeling category...
  37. pmc Novel cargo-binding site in the beta and delta subunits of coatomer
    Kai Michelsen
    Zentrum fur Molekulare Biologie der Universitat Heidelberg, Im Neuenheimer Feld 282, D 69120 Heidelberg, Germany
    J Cell Biol 179:209-17. 2007
    ..A homology model of the COPI trunk domain illustrates the recognition of R-based signals by COPI...