S
Stefan Bienert
Researcher at Swiss Institute of Bioinformatics
Publications - 11
Citations - 11544
Stefan Bienert is an academic researcher from Swiss Institute of Bioinformatics. The author has contributed to research in topics: Biology & Computer science. The author has an hindex of 7, co-authored 8 publications receiving 8164 citations. Previous affiliations of Stefan Bienert include University of Hamburg & University of Basel.
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Journal ArticleDOI
SWISS-MODEL: homology modelling of protein structures and complexes.
Andrew Waterhouse,Andrew Waterhouse,Martino Bertoni,Martino Bertoni,Stefan Bienert,Stefan Bienert,Gabriel Studer,Gabriel Studer,Gerardo Tauriello,Gerardo Tauriello,Rafal Gumienny,Rafal Gumienny,Florian T Heer,Florian T Heer,Tjaart A. P. de Beer,Tjaart A. P. de Beer,Christine Rempfer,Christine Rempfer,Lorenza Bordoli,Lorenza Bordoli,Rosalba Lepore,Rosalba Lepore,Torsten Schwede,Torsten Schwede +23 more
TL;DR: An update to the SWISS-MODEL server is presented, which includes the implementation of a new modelling engine, ProMod3, and the introduction a new local model quality estimation method, QMEANDisCo.
Journal ArticleDOI
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information
Marco Biasini,Stefan Bienert,Andrew Waterhouse,Konstantin Arnold,Gabriel Studer,Tobias Schmidt,Florian Kiefer,Tiziano Gallo Cassarino,Martino Bertoni,Lorenza Bordoli,Torsten Schwede,Torsten Schwede +11 more
TL;DR: The latest version of the SWISS-MODEL expert system for protein structure modelling is described, which makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models.
Journal ArticleDOI
ProMod3-A versatile homology modelling toolbox
Gabriel Studer,Gerardo Tauriello,Gerardo Tauriello,Stefan Bienert,Stefan Bienert,Marco Biasini,Marco Biasini,Niklaus Johner,Niklaus Johner,Torsten Schwede,Torsten Schwede +10 more
TL;DR: ProMod3 as mentioned in this paper is an open source homology modelling toolbox for protein structure modeling, which can be used for loop modelling, sidechain modelling, and generating a full protein model by homology.
Journal ArticleDOI
OpenStructure: an integrated software framework for computational structural biology
Marco Biasini,Marco Biasini,Tobias Schmidt,Tobias Schmidt,Stefan Bienert,Stefan Bienert,Valerio Mariani,Valerio Mariani,Gabriel Studer,Gabriel Studer,Juergen Haas,Juergen Haas,Niklaus Johner,Andreas D. Schenk,Ansgar Philippsen,Torsten Schwede,Torsten Schwede +16 more
TL;DR: Current developments in the computational structural biology framework OpenStructure are presented and new ideas in the framework are presented.
Journal ArticleDOI
The SIB Swiss Institute of bioinformatics' resources: Focus on curated databases
Lisandra Aguilar Bultet,José Aguilar-Rodríguez,Christian H. Ahrens,Erik Ahrné,Ni Ai,Lucila Aimo,Altuna Akalin,Tyanko Aleksiev,Davide Alocci,Adrian Altenhoff,Isabel Alves,Giovanna Ambrosini,Pascale Anderle Pedone,Paolo Angelino,Maria Anisimova,Ron Appel,Ghislaine Argoud-Puy,Konstantin Arnold,Bulak Arpat,Panu Artimo,Kelly Ascencao,Andrea H. Auchincloss,Kristian B. Axelsen,Vivienne Baillie Gerritsen,Amos Marc Bairoch,Parit Bansal,Delphine Baratin,Alessandro Barbato,Valérie Barbié,David Barras,Maria Barreiro,Sophie Barret,Frederic B. Bastian,Teresamanuela Batista Neto,Michael Baudis,Emmanuel Beaudoing,Jacques S. Beckmann,Amel Bekkar,Leila Ben Hamida Cammoun,Sara Benmohammed,Madeleine Bernard,Claire Bertelli,Martino Bertoni,Stefan Bienert,Olivier Bignucolo,Aivett Bilbao,Adem Bilican,Diana Blank,Marie Claude Blatter,Lorenz C. Blum,Jocelyne Bocquet,Brigitte Boeckmann,Jerven Bolleman,Lorenza Bordoli,Lars Bosshard,Gérard Bouchet,Lydie Bougueleret,Emmanuel Boutet,Christophe Bovigny,Sinisa Bratulic,Lionel Breuza,Alan Bridge,Aurore Britan,Francisco Brito,Josias Brito Frazão,Rémy Bruggmann,Philipp Bucher,F. Burdet,Lukas Burger,Elena Maria Cabello,Ruben Martin Cabezon Gomez,Sandra Calderon,Gina Cannarozzi,Sarah H. Carl,Cristina Casals Casas,Sebastien Catherinet,Rouayda Cavin Périer,Christophe Charpilloz,Prasad Chaskar,Wei-Hua Chen,Anush Chiappino Pepe,Bastien Chopard,Hoi Yee Chu,Natacha Civic,Manfred Claassen,Sylvie Clottu,Martino Colombo,Isabelle Cosandier,Elisabeth Coudert,Isaac Crespo,Marc Creus,Béatrice A. Cuche,Michel A. Cuendet,Isabelle Cusin,Neha Daga,Antoine Daina,Jér Ôme Dauvillier,Fabrice P. A. David,Iakov I. Davydov,Mariana De Sa Ricca Manadelo Ferreira,Tjaart A. P. de Beer,Edouard de Castro,Charles De Santana,Julien Delafontaine,Mauro Delorenzi,Céline Delucinge-Vivier,Ömer Demirel,Robert Derham,Emmanouil Manolis Dermitzakis,Linda Dib,Seydina Diene,Nahzli Dilek,Julian Dilmi,Marcin J. Domagalski,Julien Dorier,Dolnide Dornevil,Aline Dousse,René Dreos,Pablo Duchen,Paula Duek Roggli,Isabelle Dupanloup Duperret,Christine Durinx,Séverine Duvaud,Robin Engler,Serap Erkek,Pablo Escobar López,Anne Estreicher,Laurent Excoffier,Roberto Fabbretti,Jean Luc Falcone,Laurent Falquet,Maria Livia Famiglietti,Anne Maud Ferreira,M Feuermann,Marc Filliettaz,Volker Flegel,Adrien Foucal,Andrea Franceschini,Geoffrey Fucile,Dimos Gaidatzis,Victor Garcia,Elisabeth Gasteiger,Alain Gateau,Lorenzo Gatti,P Gaudet,Arnaud Gaudinat,Sebastien Gehant,David Gfeller,Walid H. Gharib,Marie Ghraichy,Cindy Gidoin,Manuel Gil,Anne Gleizes,Julien Gobeill,Gaston Gonnet,Arnaud Gos,Lou Götz,Alexandre Gouy,Djordje Grbic,Romain Groux,Nadine Gruaz-Gumowski,Delphine Grun,Andreas R. Gschwind,Nicolas Guex,Saumya Gupta,Michael Gétaz,Dennis Haake,Juergen Haas,Vassily Hatzimanikatis,Gerald Heckel,Daniel Federico Hernandez Gardiol,Valérie Hinard,Ursula Hinz,Krisztian Homicsko,Oliver Horlacher,Sayed-Rzgar Hosseini,Hans Rudolf Hotz,Chantal Hulo,Christian Hundsrucker,Mark Ibberson,Sten Ilmjärv,Vassilios Ioannidis,Panagiotis Ioannidis,Christian Iseli,Robert Ivanek,Justyna Iwaszkiewicz,Philippe Jacquet,Martin Jacquot,Vidhya Jagannathan,Maxime Jan,Jeffrey D. Jensen,Maria U. Johansson,Niklaus Johner,Florence Jungo,Thomas Junier,Abdullah Kahraman,Maria Katsantoni,Guillaume Keller,Arnaud Kerhornou,Fahad Khalid,Dirk Klingbiel,Andrea Komljenovic,Evgenia Kriventseva,Nadezda Kryuchkova,Sunil Kumar,Zoltan Kutalik,Dmitry Kuznetsov,Rostyslav Kuzyakiv,Lydie Lane,Vicente Lara,Leonardo Ledesma,Marion Leleu,P Lemercier,Daniel Lew,Damien Lieberherr,Robin Liechti,Frédérique Lisacek,Heidi E. L. Lischer,Glenn Litsios,Jialin Liu,Thierry Lombardot,Aurélien Macé,Sergio Maffioletti,Mohamed Ali Mahi,Massimo Maiolo,Somi Reddy Majjigapu,Lars Malmström,Véronique Mangold,Diana Marek,Julien Mariethoz,Ray Marin,Olivier Martin,Xavier D. Martin,Trinidad Martín-Campos,Camille Mary,Frédéric Masclaux,Patrick Masson,Cecile Meier,Antonio Messina,Muriel Metrailler Lenoir,Xavier Meyer,Pierre André Michel,Olivier Michielin,Alessio Milanese,Edoardo Missiaglia,Jorge Molina Perez,Vanessa Monteiro Caria,Philippe Moret,Sébastien Moretti,Anne Morgat,Anaïs Mottaz,Luc Mottin,Yoann Mouscaz,Markus Mueller,Riccardo Murri,Roman Mylonas,Samuel Neuenschwander,Frederic Nikitin,Anne Niknejad,Nevila Nouspikel,Lydie Nso Nso,Michal Okoniewski,Ulrich Omasits,Benjamin Paccaud,Mikhail Pachkov,Salvo Paesano,Marco Pagni,Patricia M. Palagi,Emilie Pasche,Joshua L. Payne,Ivo Pedruzzi,Stephan Peischl,Manuel C. Peitsch,Sabine Perlini,Sandrine Pilbout,Michael Podvinec,Rainer Pöhlmann,Davide Polizzi,Douglas M. Potter,Sylvain Poux,Monica Pozzato,Sylvain Pradervand,Viviane Praz,Manuela Pruess,Eva Pujadas,Julien Racle,Marcelo Raschi,Osman Ratib,Antonio Rausell,Valentine Rech De Laval,Nicole Redaschi,Christine Rempfer,Guangpeng Ren,Reza Ali Rezaee Vahdati,Leonor Rib,Oksana Riba Grognuz,Emma Ricart Altimiras,Catherine Rivoire,Thibault Robin,Marc Robinson-Rechavi,João Domingos Rodrigues,Bernd Roechert,Patrick Roelli,Valentina Romano,Grégoire Rossier,Alexander Roth,Jacques Rougemont,Julien Roux,Héléne Royo,Patrick Ruch,Michela Ruinelli,Mohamad R. Abdul Sater,Ute F. Röhrig,Sina Rüeger,Nicolas Salamin,Martial Sankar,Namrata Sarkar,Moritz Saxenhofer,Mathieu Schaeffer,Yolanda Schaerli,Elke Schaper,Annette Schmid,Emanuel Schmid,Christoph D. Schmid,Michael C. Schmid,Sebastian Schmidt,Daniel Schmocker,Michel Schneider,Thierry Schuepbach,Torsten Schwede,Frédéric Schütz,Thierry Sengstag,Martha Serrano,Atul Sethi,Omid Shahmirzadi,Christian J. A. Sigrist,Daniele Silvestro,Felipe Aristides Simao Neto,Cedric Simillion,Milan Simonovic,Nives Skunca,Kasia Sluzek,Charlotte Soneson,Kathleen Sprouffske,Michael B. Stadler,S Staehli,Brian J. Stevenson,Heinz Stockinger,Jakub Straszewski,Thomas Stricker,Gabriel Studer,Andre Stutz,Madeleine Suffiotti,Shyamala Sundaram,Damian Szklarczyk,Peter Sz Övenyi,Fredrik Tegenfeldt,Daniel Dinis Teixeira,Susanne Tellenbach,Adam Alexander T. Smith,Michael Tognolli,Ivan Topolsky,Thuong Van Du Tran,Petros Tsantoulis,Athanasia C. Tzika,Asier Ullate Agote,Erik van Nimwegen,Christian von Mering,Adithi Varadarajan,Maren Veranneman,Laure Verbregue,Anne Lise Veuthey,Dina Vishnyakova,Rounak Vyas,Andreas Wagner,Daniel Walther,Hon Wai Wan,Mingcong Wang,Robert M. Waterhouse,Andrew Waterhouse,Adrian Wicki,Leonore Wigger,Pratyaksha Wirapati,Ursula Witschi,Stefan Wyder,Kurt Wyler,Daniel Wüthrich,Ioannis Xenarios,Kana Yamada,Zheng Yan,Haleh Yasrebi,Monique Zahn,Nadine Zangger,Evgeny M. Zdobnov,Daniel Zerzion,Vincent Zoete,Stefan Zoller,Luciano Abriata,Thierry Aebischer,Murodzhon Akhmedov,Antonio Alves Meireles Filho,Stefano Andreozzi,Naara Appel,Florence Armand,Alberto J. Arribas,Samira Asgari,Meriç Ataman,Martina Audagnotto,Deniz Aydin,Pierre Bady,Claudia Bank,Diana Barac,Benoîte Bargeton,Joelle Barido-Sottani,Caterina Barillari,Istvan Bartha,Angela M. Bean,Johannes Becker,Niko Beerenwinkel,Gwendoline Bellement,Fabrizio Benedetti,Sven Bergmann,Simon Bernèche,Roel Bevers,Daniel Biasse,Manuel Bichsel,Jonathan Bieler,Ana Paula Bittencourt Piccini,Marcelo Boareto Do Amaral,Christian Bolliger,Veronika Boskova,Andrew Brown,Julien Bryois,Alfonso Buil,Rosamaria Cannavo,Mathias Cardner,Francesco Nicola Carelli,Santiago Carmona,Luciano Cascione,Anirikh Chakrabarti,Nimisha Chaturvedi,Sarvenaz Choobdar,Claire Clivaz,Simona Constantinescu,Tanguy Corre,Diego Claudio Cortez Quezada,Roberto Croce,Anne Cuendet,Jing Cui,Riccardo Dainese,Matteo Dal Peraro,Tiziano Dallavilla,Luis De Oliveira,Nicolas Delaleu,Olivier Delaneau,Bart Deplancke,Lekshmi Dharmarajan,Madeline Diekmann,Christos Dimitrakopoulos,Beatrice Dimitriades-Schmutz,Yoanaaleksandrova Dimitrova,Simon Dirmeier,Maria Pamela Dobay,Michaël Dougoud,Julien Duc,Guillaume Dumont,Louis Du Plessis,Daniel Dörr,Kristina Elfstroem,Franz Josef Elmer,Gregory B. Ewing,Imran Fanaswala,Jacques Fellay,Chrystel Feller,Georgios Fengos,Anna Ferrer,Sylvie Fiaux,Chris Field,Iris Finci,Anamarija Fofonjka,Giulia Fonti,Patrick Fried,Michael Frochaux,Juan Fuentes,Luca Galbusera,Marco Galimberti,Manuel Garcia-Albornoz,Ramón García-Escudero,Marco Garieri,Lada Georgieva,Cristina Gabriela Ghiurcuta,Souvik Ghosh,Alexandra Gnann,Robert Gnuegge,Monica Golumbeanu,Harold F. Gómez,Jér Ôme Goudet,Andreas J. Gruber,Franziska Gruhl,Sarah Guethe,Elsa Guillot,Joao C. Guimaraes,Rafal Gumienny,Rudiyanto Gunawan,Kyle Gustafson,Foivos Gypas,Noushin Hadadi,Tuure Hameri,Christian Hammer,Florian T Heer,Davide Martin Heller,Micha Hersch,Ariane Leoni Hofmann,Cédric Howald,Sandro Hutter,Dagmar Iber,Kristen K. Irwin,Katharina Jahn,Dominik J. Jedlinski,Vinay Jethava,Hadi Jorjani,Thomas Julou,Henrik Kaessmann,Alexandra Styliani Kalantzi,Alexander Kanitz,Adamandia Kapopoulou,Eleni Karamasioti,Zahra Karimaddini,Irene Keller,Alexandros Kiparissides,Manuel Kohler,Athanasios Kousathanas,Jack Kuipers,Piotr Kupczyk,Ivo Kwee,Denise Kühnert,Lakshmi Narayanan Lakshmanan,David Lamparter,Brian Lang,Sacha Laurent,Stefan Laurent,Deborah Leigh,Yu Lin,Helen Lindsay,Vivian Link,Janina Linnik,Thomas Liphardt,Yang Liu,Alexis Loetscher,Antti Olavi Luomi,Kirill Lykov,Dania Machlab,Carsten Magnus,Anne Maillard-Wermelinger,Alexander Malafeev,Anna Sapfo Malaspinas,Roger Mallol Parera,Erica Manesso,Liana Manukyan,Sarah N. Mapelli,Daniel Marbach,Maria Josefina Marcaida Lopez,Marisa Marciano Wynn,Georges Martin,António F. Martins,Katarina L. Matthes,Christian Mazza,Aaron McDaid,Jér Ôme Mermet,Odyssé Michos,Michel C. Milinkovitch,Aristotelis Misios,Ljubisa Miskovic,Venelin Mitov,Abhishek Mitra,Nitish Mittal,Hesam Montazeri,Bernard Moret,Felix Naef,Nishanth Ulhas Nair,Damien Nicolas,Stefan Nicolet,Heeju Noh,Malgorzata Nowicka,Ove Oeyaas,Saeed Omidi,Halit Ongen,Louise Ormond,Diana S. M. Ottoz,Nikolaos Panousis,Nan Papili Gao,Hassan Pezeshgi Modarres,Julija Pečerska,Joana Raquel Pinto Vieira,Igor Pivkin,Evarist Planet,Susana Posada Céspedes,Rachana Pradhan,Julien Prados,Dusan Racko,David Rasmussen,Andrea Riba,Bernd Rinn,Marion Rivoal,Mark D. Robinson,Simona W. Rossi,Fabian Rudolf,Rico Rueedi,Hans Joachim Ruscheweyh,Mikolaj Rybinski,Andrzej J. Rzepiela,Thomas Sakoparnig,Maria Magdalena San Román Rincón,Georgios Savoglidis,Petar Scepanovic,Olivier Schaad,Romy Schleiss,Fabian Schmich,Ralf Schmidt,Sara Schulthess,Petra Catalina Schwalie,David Seifert,Marianne Seijo,Mingfu Shao,Hyunjin Shim,Jochen Singer,Jonathan Sobel,Keng Cher Soh,Reyhan Sonmez Flitman,Suzanne Soto,Vitor Sousa,Tanja Stadler,Andrzej Stasiak,Ancilla Stefani,Yvonne Steger,Joerg Stelling,Anna Stopka,Isabelle Stévant,Mikael Sunnaker,Afzal Pasha Syed,Giorgio Tamo,Simon Tanaka,Grégory Theiler,Christian Axel Wandall Thorball,Thomas Thurnherr,Monica Roxana Ticlla Ccenhua,Onur Tidin,Milenko Tokic,Macarena Toll Riera,Matteo Tomasini,Stepan Tymoshenko,Minhaz Ud-Dean,Arantxa Urchueguia,Nadia Vertti Quintero,Laura Vinckenbosch,Ana Viñuela,Jannik Vollmer,Sonja Voordijk,Jingkui Wang,Zhongyi Wang,Maria Warnefors,Lukas M. Weber,Daniel Wegmann,Ellis Whitehead,Alexandre Wicky,Lukas Widmer,Min Ye,Florence Yerly,Jake Yeung,Pencho Yordanov,Mihaela Zavolan,Tobias Zehnder,Chi Zhang,Xiaobei Zhou,Aikaterini Zisaki,Benjamin Zoller,Alix Zollinger +676 more
TL;DR: An overview of S IB's resources and competence areas is provided, with a strong focus on curated databases and SIB's most popular and widely used resources.