(2021). Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance. Microorganisms, 9 (5), 1094.
(2021). ProMod3-A versatile homology modelling toolbox. PLoS computational biology, 17 (1), e1008667.
(2020). Author Correction: High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature communications, 11 (1), 5873.
(2020). High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. Nature communications, 11 (1), 5101.
(2020). A Comprehensive Mapping of the Druggable Cavities within the SARS-CoV-2 Therapeutically Relevant Proteins by Combining Pocket and Docking Searches as Implemented in Pockets 2.0. International journal of molecular sciences, 21 (14), 5152.
(2020). SPHN - The BioMedIT Network: A Secure IT Platform for Research with Sensitive Human Data. Studies in health technology and informatics, 270, 1170-1174.
(2019). Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures. Structure (London, England : 1993), 27 (12), 1745-1759.
(2019). Critical assessment of methods of protein structure prediction (CASP)-Round XIII. Proteins, 87 (12), 1011-1020.
(2019). Introducing "best single template" models as reference baseline for the Continuous Automated Model Evaluation (CAMEO). Proteins, 87 (12), 1378-1387.
(2019). Target highlights in CASP13: Experimental target structures through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 87 (12), 1037-1057.
(2019). Estimation of model accuracy in CASP13. Proteins, 87 (12), 1361-1377.
(2019). Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information. Methods in Molecular Biology, 1851, 301-316.
(2019). QMEANDisCo - Distance Constraints Applied on Model Quality Estimation. Bioinformatics, 36 (6), 1765-1771.
(2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research, 46 (W1), W296-W303.
(2018). Continuous Automated Model Evaluation (CAMEO) Complementing the Critical Assessment of Structure Prediction in CASP12. Proteins, 86 Suppl 1, 387-398.
(2018). Evaluation of the template-based modeling in CASP12. Proteins, 86 Suppl 1, 321-334.
(2018). Critical assessment of methods of protein structure prediction (CASP) - Round XII. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 7-15.
(2018). Assessment of protein assembly prediction in CASP12. Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 247-256.
(2018). A tribute to Anna Tramontano (1957-2017). Proteins: Structure, Function, and Bioinformatics, 86 (1), 5-6.
(2018). Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016). Proteins: Structure, Function, and Bioinformatics, 86 Suppl 1 (1), 27-50.
(2017). Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome medicine, 9 (1), 113.
(2017). PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models. Structure, 25 (9), 1317-1318.
(2017). Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology. Scientific Reports, 7 (1), 10480.
(2017). Assessment of model accuracy estimations in CASP12. Proteins, 86 Suppl 1 (S1), 345-360.
(2017). Anna Tramontano 1957-2017. Nature Structural and Molecular Biology, 24 (5), 431-432.
(2017). Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein. mBio, 8 (2), e00294-17.
(2017). A computational protocol to evaluate the effects of protein mutants in the kinase gatekeeper position on the binding of ATP substrate analogues. BMC Research Notes, 10 (1), 104.
(2017). The SWISS-MODEL Repository - new features and functionality. Nucleic Acids Research, 45 (D1), D313-D319.
(2017). 2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update. Acta Crystallographica Section D, 73 (Pt9), 710-728.
(2017). Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public. Journal of Chemical Education, 94 (3), 335-344.
(2017). Exome sequencing of healthy phenotypic extremes links TROVE2 to emotional memory and PTSD. Nature Human Behaviour, 1, 0081.
(2016). Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae. The Lancet Infectious Diseases, 16 (9), 998-999.
(2016). Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances, 2 (9), e1600823.
(2016). Making sense of big data in health research: Towards an EU action plan. Genome medicine, 8 (1), 71.
(2016). Critical assessment of methods of protein structure prediction: Progress and new directions in round XI. Proteins: Structure, Function, and Bioinformatics, 84 Suppl 1 (1), 4-14.
(2016). The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases. Nucleic acids research, 44 (D1), D27-D37.
(2016). Some of the most interesting CASP11 targets through the eyes of their authors. Proteins: Structure, Function, and Bioinformatics, 84 (1), 34-50.
(2016). Methods of model accuracy estimation can help selecting the best models from decoy sets: Assessment of model accuracy estimations in CASP11. Proteins, 84 (Suppl1), 349-69.
(2015). Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop. Structure: with folding and design, 23 (7), 1156-67.
(2015). Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering. Open biology, 5 (4), 140227.
(2015). Data to knowledge: how to get meaning from your result. IUCrJ, 2 (Pt1), 45-58.
(2014). Computational Analysis of Methyl Transfer Reactions in Dengue Virus Methyltransferase. Journal of Physical Chemistry B, 118 (22), 5882-5890.
(2014). Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support. Nucleic Acids Research, 42 (WebServerissue), W436-41.
(2014). SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42 (WebServerissue), W252-8.
(2014). Critical assessment of methods of protein structure prediction (CASP) - round X. Proteins, 82 Suppl 2 (S2), 1-6.
(2014). Challenging the state-of-the-art in protein structure prediction : highlights of experimental target structures for the 10(th) Critical Assessment of Techniques for Protein Structure Prediction Experiment CASP10. Proteins, 82 (S2), 26-42.
(2014). Modelling three-dimensional protein structures for applications in drug design. Drug discovery today, 19 (7), 890-7.
(2014). Assessment of the assessment : evaluation of the model quality estimates in CASP10. Proteins, 82 Suppl 2 (S2), 112-26.
(2014). Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). Bioinformatics, 30 (17), i505-11.
(2014). Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage. Biospektrum, 20 (2), 236-237.
(2014). Assessment of ligand binding site predictions in CASP10. Proteins, 82 Suppl 2 (S2), 154-63.
(2013). Protein modeling: what happened to the "protein structure gap"?. Structure: with folding and design, 21 (9), 1531-1540.
(2013). lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests. Bioinformatics, 29 (21), 2722-8.
(2013). OpenStructure : an integrated software framework for computational structural biology. Acta crystallographica. Section D, Biological crystallography, 69 (Pt5), 701-9.
(2013). Report of the wwPDB Small-Angle Scattering Task Force : data requirements for biomolecular modeling and the PDB. Structure: with folding and design, 21 (6), 875-81.
(2013). The Protein Model Portal: a comprehensive resource for protein structure and model information. Database, 2013, bat031.
(2013). Homology Modeling of Protein Structures. , in: Roberts, G.C.K.Encyclopedia of Biophysics, Berlin: Springer, 992-998.
(2012). ECCB 2012 : The 11th European Conference on Computational Biology. Bioinformatics, 28 (18), i303-i305.
(2012). Improving your target-template alignment with MODalign. Bioinformatics, 28 (7), 1038-9.
: Automated Protein Structure Modeling with SWISS-MODEL Workspace and the Protein Model Portal, in: Orry, Andrew JW; Abagyan, Ruben(Ed.). (2012). Homology Modeling: Methods and Protocols, New York, USA: Humana Press, Vol. 857, S.107-36.
(2011). Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins: Structure, Function, and Bioinformatics, 79 Suppl 10 (S10), 6-20.
(2011). Assessment of template based protein structure predictions in CASP9. Proteins, 79 Suppl 10 (S10), 37-58.
(2011). CASP9 target classification. Proteins, 79 (s10), 21-36.
(2011). Assessment of ligand-binding residue predictions in CASP9. Proteins, 79 Suppl 10 (S10), 126-36.
(2011). The Structural Biology Knowledgebase : a portal to protein structures, sequences, functions, and methods. Journal of structural and functional genomics, 12 (2), 45-54.
(2011). The Mouse Eugenol Odorant Receptor : Structural and Functional Plasticity of a Broadly Tuned Odorant Binding Pocket. Biochemistry, 50 (5), 843-53.
(2011). Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 27 (3), 343-50.
(2010). OpenStructure: a flexible software framework for computational structural biology. Bioinformatics, 26 (20), 2626-8.
(2010). Novel Inhibitors of Dengue Virus Methyltransferase : discovery by in vitro-driven virtual screening on a Desktop Computer Grid. Journal of Medicinal Chemistry, 53 (4), 1483-95.
(2010). Protein Homology Modelling - Providing Three-dimensional Models for Proteins where Experimental Data is Missing. ERCIM News, 82, 20-21.
(2009). Dual activities of odorants on olfactory and nuclear hormone receptors. Journal of biological chemistry, 284 (44), 30547-55.
(2009). Global and local model quality estimation at CASP8 using the scoring functions QMEAN and QMEANclust. Proteins, 77 Suppl 9 (S9), 173-80.
(2009). QMEAN server for protein model quality estimation. Nucleic Acids Research, 37 (WebServerissue), W510-4.
: Protein Structure Modeling and Docking at the Swiss Institute of Bioinformatics, in: Appel, RD; Feytmans, E.(Ed.). (2009). Bioinformatics. A Swiss Perspective, New Jersey: World Scientific, S.219-246.
(2009). Protein structure homology modelling using SWISS-MODEL Workspace. Nature Protocols, 4 (1), 1-13.
(2009). The protein structure initiative structural genomics knowledgebase. Nucleic Acids Research, 37 (1Supplement), D365-D368.
(2009). Second messenger-mediated spatiotemporal control of protein degradation regulates bacterial cell cycle progression. Genes & development, 23 (1), 93-104.
(2009). The Swiss-model Repository and associated resources. Nucleic Acids Research, 37 (1Supplement), D387-D392.
(2009). Outcome of a workshop on applications of protein models in biomedical research. Structure, 17 (2), 151-9.
(2009). QMEANclust : estimation of protein model quality by combining a composite scoring function with structural density information. BMC Structural Biology, 9 (1), 35.
(2009). Automated comparative protein structure modeling with Swiss-model and Swiss-PdbViewer : a historical perspective. Electrophoresis, 30 Suppl 1 (S1), S162-73.
(2009). The protein model portal. Journal of structural and functional genomics, 10 (1), 1-8.
: Protein Structure Modeling, in: Schwede, T.; Peitsch, M.C.(Ed.). (2008). Computational structural biology, Singapore: World Scientific, S.700.
: Docking for neglected diseases as community efforts, in: Schwede T,; Peitsch MC,(Ed.). (2008). Computational structural biology, Singapore: World Scientific Publishing, S.683-704.
(2007). Tandem mass spectrometry protein identification on a PC grid. Studies in health technology and informatics, 126, 3-12.
(2007). Assessment of CASP7 predictions for template-based modeling targets. Proteins, 69 Suppl 8, 38-56.
(2007). Assessment of disorder predictions in CASP7. Proteins, 69 Suppl 8, 129-36.
(2007). Automated server predictions in CASP7. Proteins, 69 Suppl 8, 68-82.
(2007). Novel cargo-binding site in the beta and delta subunits of coatomer. The Journal of cell biology, 179 (2), 209-17.
(2007). Domain Definition and Target Classification for CASP7. Proteins, 69 Suppl 8 (S8), 10-8.
(2007). Sulfonylureas and glinides exhibit peroxisome proliferator-activated receptor gamma activity : a combined virtual screening and biological assay approach. Molecular pharmacology, 71 (2), 398-406.
: SWISS-TANDEM : a Web-based workspace for MS/MS protein identification on PC grid, in: Kokol, P; Podgorelec, V; MiceticTurk, D; Zorman, M; Verlic, M(Ed.). (2007). Twentieth IEEE international symposium on computer-based medical systems, Los Alamitos, Calif.: IEEE Computer Society, CBMS 2007.
(2007). Mutations in the Sec61p channel affecting signal sequence recognition and membrane protein topology. Journal of biological chemistry, 282 (45), 33201-9.
: The SwissBioGrid Project : objectives, preliminary results and lessons learnede-Science 2006 : 2nd IEEE International Conference on e-Science and Grid Computing, Los Alamitos, Calif.: IEEE Computer Society, e-Science 2006, 148.
(2006). Outcome of a workshop on archiving structural models of biological macromolecules. Structure: with folding and design, 14 (8), 1211-7.
(2006). The Swiss-model Repository : new features and functionalities. Nucleic Acids Research, 34 (D1), D315-D318.
(2006). The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics, 22 (2), 195-201.
(2006). The plug domain of yeast Sec61p is important for efficient protein translocation, but is not essential for cell viability. Molecular Biology of the Cell, 17 (9), 4063-4068.
(2004). The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Research, 32 (1Supplement), D230-D234.
(2004). Automated protein structure homology modeling : a progress report. Pharmacogenomics, 5 (4), 405-16.
(2003). Swiss-model : an automated protein homology-modeling server. Nucleic Acids Research, 31 (13), 3381-5.
(2003). Covalent and three-dimensional structure of the cyclodextrinase from Flavobacterium sp. no. 92. European journal of biochemistry, 270 (10), 2332-41.
(2003). Asp1424Asn MYH9 mutation results in an unstable protein responsible for the phenotypes in May-Hegglin anomaly/Fechtner syndrome. Blood, 102 (2), 529-34.
: Protein Structure Modeling in Functional GenomicsFrontiers in Computational Genomics, Horizon Scientific Press: Horizon Scientific Press.
: Imaging science in biochemistry, in: Hornak, Joseph P.(Ed.). (2002). Encyclopedia of imaging science and technology, New York: John Wiley & Sons, n.a.(onlinebook).
(2002). Mutations in the TMPRSS3 gene are a rare cause of childhood non-syndromic deafness in Caucasian patients. Journal of molecular medicine, 80, 124-131.
(2001). Novel missense mutations of TMPRSS3 in two consanguineous Tunisian families with non-syndromic autosomal recessive deafness. Human mutation, 18 (2), 101-8.
(2000). Automated protein modelling-the proteome in 3D. Pharmacogenomics, 1 (3), 257-66.
(2000). Protein structure computing in the genomic era. Research in microbiology, 151 (2), 107-12.
: Protein Tertiary Structure ModelingCurrent Protocols in Protein Science, [New York]: Wiley, nit 2.8.1-2.8.17, 2.8.1-2.8.17.
(1999). Crystal Structure of Histidine Ammonia-Lyase Revealing a Novel Polypeptide Modification as the Catalytic Electrophile. Biochemistry, 38 (17), 5355-61.
(1999). Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue. Protein Engineering, 12 (2), 151-3.