Publications

Righetto, R. D., Anton, L., Adaixo, R., Jakob, R. P., Zivanov, J., Mahi, M.-A., Ringler, P., Schwede, T., Maier, T. und Stahlberg, H. (2020) «High-resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica». bioRxiv. doi: 10.1101/2020.04.28.065599.   
Cheng, J., Choe, M.-H., Elofsson, A., Han, K.-S., Hou, J., Maghrabi, A. H. A., McGuffin, L. J., Menéndez-Hurtado, D., Olechnovič, K., Schwede, T., Studer, G., Uziela, K., Venclovas, Česlovas und Wallner, B. (2019) «Estimation of model accuracy in CASP13», Proteins. Wiley-Blackwell, 87(12), S. 1361-1377. doi: 10.1002/prot.25767.   edoc
Studer, G., Tauriello, G., Bienert, S., Waterhouse, A. M., Bertoni, M., Bordoli, L., Schwede, T. und Lepore, R. (2019) «Modeling of Protein Tertiary and Quaternary Structures Based on Evolutionary Information», Methods in Molecular Biology. Humana Press, 1851, S. 301-316. doi: 10.1007/978-1-4939-8736-8_17.   edoc
Berman, H. M., Adams, P. D., Bonvin, A. A., Burley, S. K., Carragher, B., Chiu, W., DiMaio, F., Ferrin, T. E., Gabanyi, M. J., Goddard, T. D., Griffin, P. R., Haas, J., Hanke, C. A., Hoch, J. C., Hummer, G., Kurisu, G., Lawson, C. L., Leitner, A., Markley, J. L., Meiler, J., Montelione, G. T., Phillips, G. N., Prisner, T., Rappsilber, J., Schriemer, D. C., Schwede, T., Seidel, C. A. M., Strutzenberg, T. S., Svergun, D. I., Tajkhorshid, E., Trewhella, J., Vallat, B., Velankar, S., Vuister, G. W., Webb, B., Westbrook, J. D., White, K. L. und Sali, A. (2019) «Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures», Structure (London, England : 1993), 27(12), S. 1745-1759. doi: 10.1016/j.str.2019.11.002.   
Lepore, R., Kryshtafovych, A., Alahuhta, M., Veraszto, H. A., Bomble, Y. J., Bufton, J. C., Bullock, A. N., Caba, C., Cao, H., Davies, O. R., Desfosses, A., Dunne, M., Fidelis, K., Goulding, C. W., Gurusaran, M., Gutsche, I., Harding, C. J., Hartmann, M. D., Hayes, C. S., Joachimiak, A., Leiman, P. G., Loppnau, P., Lovering, A. L., Lunin, V. V., Michalska, K., Mir-Sanchis, I., Mitra, A., Moult, J., Phillips, G. N., Pinkas, D. M., Rice, P. A., Tong, Y., Topf, M., Walton, J. D. und Schwede, T. (2019) «Target highlights in CASP13: Experimental target structures through the eyes of their authors», Proteins, 87(12), S. 1037-1057. doi: 10.1002/prot.25805.   
Studer, G., Rempfer, C., Waterhouse, A. M., Gumienny, R., Haas, J. und Schwede, T. (2019) «QMEANDisCo - Distance Constraints Applied on Model Quality Estimation», Bioinformatics, S. epubaheadofrint. doi: 10.1093/bioinformatics/btz828.   
Kryshtafovych, A., Schwede, T., Topf, M., Fidelis, K. und Moult, J. (2019) «Critical assessment of methods of protein structure prediction (CASP)-Round XIII», Proteins, 87(12), S. 1011-1020. doi: 10.1002/prot.25823.   
Haas, J., Gumienny, R., Barbato, A., Ackermann, F., Tauriello, G., Bertoni, M., Studer, G., Smolinski, A. und Schwede, T. (2019) «Introducing ‹best single template› models as reference baseline for the Continuous Automated Model Evaluation (CAMEO)», Proteins, 87(12), S. 1378-1387. doi: 10.1002/prot.25815.   
Haas, J., Barbato, A., Behringer, D., Studer, G., Roth, S., Bertoni, M., Mostaguir, K., Gumienny, R. und Schwede, T. (2018) «Continuous Automated Model Evaluation (CAMEO) Complementing the Critical Assessment of Structure Prediction in CASP12», Proteins, 86 Suppl 1, S. 387-398. doi: 10.1002/prot.25431.   edoc
Kryshtafovych, A., Monastyrskyy, B., Fidelis, K., Moult, J., Schwede, T. und Tramontano, A. (2018) «Evaluation of the template-based modeling in CASP12», Proteins, 86 Suppl 1, S. 321-334. doi: 10.1002/prot.25425.   edoc
Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., Heer, F. T., de Beer, T. A. P., Rempfer, C., Bordoli, L., Lepore, R. und Schwede, T. (2018) «SWISS-MODEL: homology modelling of protein structures and complexes», Nucleic acids research, 46(W1), S. W296-W303. doi: 10.1093/nar/gky427.   edoc
Moult, J., Fidelis, K., Kryshtafovych, A. und Schwede, T. (2018) «A tribute to Anna Tramontano (1957-2017)», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 86(1), S. 5-6. doi: 10.1002/prot.25406.   edoc
Lafita, A., Bliven, S., Kryshtafovych, A., Bertoni, M., Monastyrskyy, B., Duarte, J. M., Schwede, T. und Capitani, G. (2018) «Assessment of protein assembly prediction in CASP12», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 86(1), S. 247-256. doi: 10.1002/prot.25408.   edoc
Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T. und Tramontano, A. (2018) «Critical assessment of methods of protein structure prediction (CASP) - Round XII», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 86(1), S. 7-15. doi: 10.1002/prot.25415.   edoc
Kryshtafovych, A., Albrecht, R., Baslé, A., Bule, P., Caputo, A. T., Carvalho, A. L., Chao, K. L., Diskin, R., Fidelis, K., Fontes, C. M. G. A., Fredslund, F., Gilbert, H. J., Goulding, C. W., Hartmann, M. D., Hayes, C. S., Herzberg, O., Hill, J. C., Joachimiak, A., Kohring, G.-W., Koning, R. I., Lo Leggio, L., Mangiagalli, M., Michalska, K., Moult, J., Najmudin, S., Nardini, M., Nardone, V., Ndeh, D., Nguyen, T.-H., Pintacuda, G., Postel, S., van Raaij, M. J., Roversi, P., Shimon, A., Singh, A. K., Sundberg, E. J., Tars, K., Zitzmann, N. und Schwede, T. (2018) «Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 86(1), S. 27-50. doi: 10.1002/prot.25392.   edoc | Open Access
Glusman, G., Rose, P. W., Prlić, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T., Karchin, R., Leman, J. K., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. und Deutsch, E. W. (2017) «Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework», Genome medicine. BioMed Central, 9(1), S. 113. doi: 10.1186/s13073-017-0509-y.   edoc
Kryshtafovych, A., Monastyrskyy, B., Fidelis, K., Schwede, T. und Tramontano, A. (2017) «Assessment of model accuracy estimations in CASP12», Proteins. Wiley, 86(S1), S. 345-360. doi: 10.1002/prot.25371.   edoc
Burley, S. K., Kurisu, G., Markley, J. L., Nakamura, H., Velankar, S., Berman, H. M., Sali, A., Schwede, T. und Trewhella, J. (2017) «PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models», Structure . Elsevier, 25(9), S. 1317-1318. doi: 10.1016/j.str.2017.08.001.   edoc
Daina, A., Blatter, M.-C., Baillie Gerritsen, V., Palagi, P. M., Marek, D., Xenarios, I., Schwede, T., Michielin, O. und Zoete, V. (2017) «Drug Design Workshop: A Web-Based Educational Tool To Introduce Computer-Aided Drug Design to the General Public», Journal of Chemical Education. American Chemical Society, 94(3), S. 335-344. doi: 10.1021/acs.jchemed.6b00596.   edoc
Thornton, J. M., Valencia, A. und Schwede, T. (2017) «Anna Tramontano 1957-2017», Nature Structural and Molecular Biology. Nature Publishing Group , 24(5), S. 431-432. doi: 10.1038/nsmb.3410.   edoc
Bertoni, M., Kiefer, F., Biasini, M., Bordoli, L. und Schwede, T. (2017) «Modeling protein quaternary structure of homo- and hetero-oligomers beyond binary interactions by homology», Scientific Reports. Nature Publishing Group, 7(1), S. 10480. doi: 10.1038/s41598-017-09654-8.   edoc
Trewhella, J., Duff, A. P., Durand, D., Gabel, F., Guss, J. M., Hendrickson, W. A., Hura, G. L., Jacques, D. A., Kirby, N. M., Kwan, A. H., P`erezJ., Pollack, L., Ryan, T. M., Sali, A., Schneidman-Duhovny, D., Schwede, T., Svergun, D. I., Sugiyama, M., Tainer, J. A., Vachette, P., Westbrook, J. und Whitten, A. E. (2017) «2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update», Acta Crystallographica Section D. Wiley-Blackwell Publishing, 73(9), S. 710-728. doi: 10.1107/S2059798317011597.   edoc
Sprecher, K. S., Hug, I., Nesper, J., Potthoff, E., Mahi, M.-A., Sangermani, M., Kaever, V., Schwede, T., Vorholt, J. und Jenal, U. (2017) «Cohesive Properties of the Caulobacter crescentus Holdfast Adhesin Are Regulated by a Novel c-di-GMP Effector Protein», mBio. American Society for Microbiology, 8(2), S. e00294-17. doi: 10.1128/mBio.00294-17.   edoc | Open Access
Romano, V., de Beer, T. A. P. und Schwede, T. (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. BioMed Central, 10(1), S. 104. doi: 10.1186/s13104-017-2428-9.   edoc
Bienert, S., Waterhouse, A., de Beer, T. A. P., Tauriello, G., Studer, G., Bordoli, L. und Schwede, T. (2017) «The SWISS-MODEL Repository - new features and functionality», Nucleic Acids Research. Oxford University Press, 45(D1), S. D313-D319. doi: 10.1093/nar/gkw1132.   edoc | Open Access
Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T. und Tramontano, A. (2016) «Critical assessment of methods of protein structure prediction (CASP) - progress and new directions in Round XI», Proteins. Wiley-Liss, S. 4-14. doi: 10.1002/prot.25064.   edoc
Swiss Institute of Bioinformatics Members, S. (2016) «The SIB Swiss Institute of Bioinformatics’ resources: focus on curated databases», Nucleic acids research. Oxford University Press, 44(D1), S. D27-D37. doi: 10.1093/nar/gkv1310.   edoc | Open Access
Nicolet, S., Goldenberger, D., Schwede, T., Page, M. und Creus, M. (2016) «Plasmid-mediated colistin resistance in a patient infected with Klebsiella pneumoniae», The Lancet Infectious Diseases. Elsevier, S. 998-999. doi: 10.1016/S1473-3099(16)30197-9.   edoc
Moult, J., Fidelis, K., Kryshtafovych, A., Schwede, T. und Tramontano, A. (2016) «Critical assessment of methods of protein structure prediction: Progress and new directions in round XI», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 84(1), S. 4-14. doi: 10.1002/prot.25064.   edoc
Kryshtafovych, A., Moult, J., Baslé, A., Burgin, A., Craig, T. K., Edwards, R. A., Fass, D., Hartmann, M. D., Korycinski, M., Lewis, R. J., Lorimer, D., Lupas, A. N., Newman, J., Peat, T. S., Piepenbrink, K. H., Prahlad, J., van Raaij, M. J., Rohwer, F., Segall, A. M., Seguritan, V., Sundberg, E. J., Singh, A. K., Wilson, M. A. und Schwede, T. (2016) «Some of the most interesting CASP11 targets through the eyes of their authors», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 84(1), S. 34-50. doi: 10.1002/prot.24942.   edoc
Auffray, C., Balling, R., Barroso, I., Bencze, L., Benson, M., Bergeron, J., Bernal-Delgado, E., Blomberg, N., Bock, C., Conesa, A., Del Signore, S., Delogne, C., Devilee, P., Di Meglio, A., Eijkemans, M., Flicek, P., Graf, N., Grimm, V., Guchelaar, H.-J., Guo, Y.-K., Gut, I. G., Hanbury, A., Hanif, S., Hilgers, R.-D., Honrado, Ángel, Hose, D. R., Houwing-Duistermaat, J., Hubbard, T., Janacek, S. H., Karanikas, H., Kievits, T., Kohler, M., Kremer, A., Lanfear, J., Lengauer, T., Maes, E., Meert, T., Müller, W., Nickel, D., Oledzki, P., Pedersen, B., Petkovic, M., Pliakos, K., Rattray, M., I. Màs, J. R., Schneider, R., Sengstag, T., Serra-Picamal, X., Spek, W., Vaas, L. A. I., van Batenburg, O., Vandelaer, M., Varnai, P., Villoslada, P., Vizcaíno, J. A., Wubbe, J. P. M. und Zanetti, G. (2016) «Making sense of big data in health research: Towards an EU action plan», Genome medicine, 8(1), S. 71. doi: 10.1186/s13073-016-0323-y.   edoc
Kryshtafovych, A., Barbato, A., Monastyrskyy, B., Fidelis, K., Schwede, T. und Tramontano, A. (2016) «Methods of model accuracy estimation can help selecting the best models from decoy sets: assessment of model accuracy estimations in CASP11», Proteins: Structure, Function, and Bioinformatics . Wiley-Blackwell, 84(1), S. 349-369. doi: 10.1002/prot.24919.   edoc
Sali, A., Berman, H. M., Schwede, T., Trewhella, J., Kleywegt, G., Burley, S. K., Markley, J., Nakamura, H., Adams, P., Bonvin, A. M. J. J., Chiu, W., Peraro, M. D., Di Maio, F., Ferrin, T. E., Grünewald, K., Gutmanas, A., Henderson, R., Hummer, G., Iwasaki, K., Johnson, G., Lawson, C. L., Meiler, J., Marti-Renom, M. A., Montelione, G. T., Nilges, M., Nussinov, R., Patwardhan, A., Rappsilber, J., Read, R. J., Saibil, H., Schröder, G. F., Schwieters, C. D., Seidel, C. A. M., Svergun, D., Topf, M., Ulrich, E. L., Velankar, S. und Westbrook, J. D. (2015) «Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop», Structure: with folding and design. Current Biology, 23(7), S. 1156-1167. doi: 10.1016/j.str.2015.05.013.   edoc
Ihssen, J., Haas, J., Kowarik, M., Wiesli, L., Wacker, M., Schwede, T. und Thöny-Meyer, L. (2015) «Increased efficiency of Campylobacter jejuni N-oligosaccharyltransferase PglB by structure-guided engineering», Open biology. Royal Society Pub., 5(4), S. 140227. doi: 10.1098/rsob.140227.   edoc
Berman, H. M., Gabanyi, M. J., Groom, C. R., Johnson, J. E., Murshudov, G. N., Nicholls, R. A., Reddy, V., Schwede, T., Zimmerman, M. D., Westbrook, J. und Minor, W. (2015) «Data to knowledge: how to get meaning from your result», IUCrJ. International Union of Crystallography, 2(Pt 1), S. 45-58. doi: 10.1107/S2052252514023306.   edoc
Haas, J. und Schwede, T. (2014) «Unabhängige Validierung von Methoden zur Proteinstrukturvorhersage», Biospektrum. Springer Spektrum, 20(2), S. 236-237. doi: 10.1007/s12268-014-0432-3.   edoc
Uda, N. R., Upert, G., Angelici, G., Nicolet, S., Schmidt, T., Schwede, T. und Creus, M. (2014) «Zinc-selective inhibition of the promiscuous bacterial amide-hydrolase DapE: implications of metal heterogeneity for evolution and antibiotic drug design», Metallomics. Royal Society of Chemistry, 6(1), S. 88-95. doi: 10.1039/c3mt00125c.   edoc | Open Access
Studer, G., Biasini, M. und Schwede, T. (2014) «Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane)», Bioinformatics. Oxford University Press, 30(17), S. i505-11. doi: 10.1093/bioinformatics/btu457.   edoc
Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L. und Schwede, T. (2014) «SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information», Nucleic Acids Research. Oxford University Press, 42(W1), S. W252-W258. doi: 10.1093/nar/gku340.   edoc | Open Access
Stockinger, H., Altenhoff, A. M., Arnold, K., Bairoch, A., Bastian, F., Bergmann, S., Bougueleret, L., Bucher, P., Delorenzi, M., Lane, L., Mercier, P. L., Lisacek, F., Michielin, O., Palagi, P. M., Rougemont, J., Schwede, T., Mering, C. von, Nimwegen, E. van, Walther, D., Xenarios, I., Zavolan, M., Zdobnov, E. M., Zoete, V. und Appel, R. D. (2014) «Fifteen years SIB Swiss Institute of Bioinformatics : life science databases, tools and support», Nucleic Acids Research. Oxford University Press, 42(W1), S. W436-W441. doi: 10.1093/nar/gku380.   edoc | Open Access