Affiliation: University of Basel
- 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....
- SWISS-MODEL: An automated protein homology-modeling serverTorsten 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...
- Outcome of a workshop on applications of protein models in biomedical researchTorsten Schwede
Swiss Institute of Bioinformatics, Biozentrum, University of Basel, Klingelbergstrasse 50 70, CH 4056 Basel, Switzerland
Structure 17:151-9. 2009....
- The Protein Model PortalKonstantin 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...
- Protein structure homology modeling using SWISS-MODEL workspaceLorenza 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...
- Assessment of template based protein structure predictions in CASP9Valerio 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...
- The SWISS-MODEL Repository and associated resourcesFlorian 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...
- Automated server predictions in CASP7James 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...
- The Protein Model Portal--a comprehensive resource for protein structure and model informationJuergen 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...
- Automated comparative protein structure modeling with SWISS-MODEL and Swiss-PdbViewer: a historical perspectiveNicolas 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...
- Assessment of ligand-binding residue predictions in CASP9Tobias Schmidt
Biozentrum, University of Basel, SIB Swiss Institute of Bioinformatics, Klingelbergstrasse 50 70, Basel, Switzerland
Proteins 79:126-36. 2011....
- Assessment of disorder predictions in CASP7Lorenza Bordoli
Biozentrum University of Basel, Basel, Switzerland
Proteins 69:129-36. 2007....
- The SWISS-MODEL Repository: new features and functionalitiesJurgen 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/...
- Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclustPascal 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/...
- The SWISS-MODEL Repository of annotated three-dimensional protein structure homology modelsJurgen 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...
- Improving your target-template alignment with MODalignAlessandro 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...
- Novel inhibitors of dengue virus methyltransferase: discovery by in vitro-driven virtual screening on a desktop computer gridMichael 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...
- Automated protein structure homology modeling: a progress reportJurgen 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...
- QMEANclust: estimation of protein model quality by combining a composite scoring function with structural density informationPascal 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...
- QMEAN server for protein model quality estimationPascal 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...
- How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor bindingHolmfridur B Thorsteinsdottir
Biozentrum, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland
Proteins 65:407-23. 2006....
- Assessment of CASP7 predictions for template-based modeling targetsJurgen 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...
- Toward the estimation of the absolute quality of individual protein structure modelsPascal 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...
- OpenStructure: a flexible software framework for computational structural biologyMarco 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...
- Assessment of ligand binding site predictions in CASP10Tiziano Gallo Cassarino
Biozentrum, University of Basel, Basel, Switzerland SIB Swiss Institute of Bioinformatics, Basel, Switzerland
Proteins 82:154-63. 2014....
- lDDT: a local superposition-free score for comparing protein structures and models using distance difference testsValerio 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...
- Automated protein structure modeling with SWISS-MODEL Workspace and the Protein Model PortalLorenza 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...
- Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity: a combined virtual screening and biological assay approachMarco 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...
- Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progressionAnna 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...
- Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug designNarasimha 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...
- The SWISS-MODEL workspace: a web-based environment for protein structure homology modellingKonstantin Arnold
Biozentrum Basel, University of Basel Switzerland
Bioinformatics 22:195-201. 2006....
- Domain definition and target classification for CASP7Neil 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...
- Novel cargo-binding site in the beta and delta subunits of coatomerKai 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...
- Outcome of a workshop on archiving structural models of biological macromoleculesHelen 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