Computational protein design quantifies structural constraints on amino acid covariation.

by Noah Ollikainen, Tanja Kortemme
Published 2013-01-01

Improvements to robotics-inspired conformational sampling in rosetta.

by Amelie Stein, Tanja Kortemme
Published 2013-01-01

Design of multi-specificity in protein interfaces.

by Elisabeth L Humphris, Tanja Kortemme
Published 2007-08-01

New computational protein design methods for de novo small molecule binding sites.

by James E Lucas, Tanja Kortemme
Published 2020-10-01

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

by Colin A Smith, Tanja Kortemme
Published 2011-01-01

Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity.

by Noah Ollikainen, René M de Jong, Tanja Kortemme
Published 2015-01-01

Altered expression of a quality control protease in E. coli reshapes the in vivo mutational landscape of a model enzyme

by Samuel Thompson, Yang Zhang, Christine Ingle, Kimberly A Reynolds, Tanja Kortemme
Published 2020-07-01

Prediction of mutational tolerance in HIV-1 protease and reverse transcriptase using flexible backbone protein design.

by Elisabeth Humphris-Narayanan, Eyal Akiva, Rocco Varela, Shane Ó Conchúir, Tanja Kortemme
Published 2012-01-01

A correspondence between solution-state dynamics of an individual protein and the sequence and conformational diversity of its family.

by Gregory D Friedland, Nils-Alexander Lakomek, Christian Griesinger, Jens Meiler, Tanja Kortemme
Published 2009-05-01

Amino-acid site variability among natural and designed proteins

by Eleisha L. Jackson, Noah Ollikainen, Arthur W. Covert III, Tanja Kortemme, Claus O. Wilke
Published 2013-11-01

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

by Shane Ó Conchúir, Kyle A Barlow, Roland A Pache, Noah Ollikainen, Kale Kundert, Matthew J O'Meara, Colin A Smith, Tanja Kortemme
Published 2015-01-01

Deconstruction of the Ras switching cycle through saturation mutagenesis

by Pradeep Bandaru, Neel H Shah, Moitrayee Bhattacharyya, John P Barton, Yasushi Kondo, Joshua C Cofsky, Christine L Gee, Arup K Chakraborty, Tanja Kortemme, Rama Ranganathan, John Kuriyan
Published 2017-07-01

Quantitative mapping of protein-peptide affinity landscapes using spectrally encoded beads

by Huy Quoc Nguyen, Jagoree Roy, Björn Harink, Nikhil P Damle, Naomi R Latorraca, Brian C Baxter, Kara Brower, Scott A Longwell, Tanja Kortemme, Kurt S Thorn, Martha S Cyert, Polly Morrell Fordyce
Published 2019-07-01

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

by Kale Kundert, James E. Lucas, Kyle E. Watters, Christof Fellmann, Andrew H. Ng, Benjamin M. Heineike, Christina M. Fitzsimmons, Benjamin L. Oakes, Jiuxin Qu, Neha Prasad, Oren S. Rosenberg, David F. Savage, Hana El-Samad, Jennifer A. Doudna, Tanja Kortemme
Published 2019-05-01

Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE).

by Sergey Lyskov, Fang-Chieh Chou, Shane Ó Conchúir, Bryan S Der, Kevin Drew, Daisuke Kuroda, Jianqing Xu, Brian D Weitzner, P Douglas Renfrew, Parin Sripakdeevong, Benjamin Borgo, James J Havranek, Brian Kuhlman, Tanja Kortemme, Richard Bonneau, Jeffrey J Gray, Rhiju Das
Published 2013-01-01

Better together: Elements of successful scientific software development in a distributed collaborative community.

by Julia Koehler Leman, Brian D Weitzner, P Douglas Renfrew, Steven M Lewis, Rocco Moretti, Andrew M Watkins, Vikram Khipple Mulligan, Sergey Lyskov, Jared Adolf-Bryfogle, Jason W Labonte, Justyna Krys, RosettaCommons Consortium, Christopher Bystroff, William Schief, Dominik Gront, Ora Schueler-Furman, David Baker, Philip Bradley, Roland Dunbrack, Tanja Kortemme, Andrew Leaver-Fay, Charlie E M Strauss, Jens Meiler, Brian Kuhlman, Jeffrey J Gray, Richard Bonneau
Published 2020-05-01

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

by David Mavor, Kyle Barlow, Samuel Thompson, Benjamin A Barad, Alain R Bonny, Clinton L Cario, Garrett Gaskins, Zairan Liu, Laura Deming, Seth D Axen, Elena Caceres, Weilin Chen, Adolfo Cuesta, Rachel E Gate, Evan M Green, Kaitlin R Hulce, Weiyue Ji, Lillian R Kenner, Bruk Mensa, Leanna S Morinishi, Steven M Moss, Marco Mravic, Ryan K Muir, Stefan Niekamp, Chimno I Nnadi, Eugene Palovcak, Erin M Poss, Tyler D Ross, Eugenia C Salcedo, Stephanie K See, Meena Subramaniam, Allison W Wong, Jennifer Li, Kurt S Thorn, Shane Ó Conchúir, Benjamin P Roscoe, Eric D Chow, Joseph L DeRisi, Tanja Kortemme, Daniel N Bolon, James S Fraser
Published 2016-04-01

Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance

by David Mavor, Kyle A. Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M. Green, Lillian R. Kenner, Bruk Mensa, Leanna S. Morinishi, Charlotte A. Nelson, Erin M. Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice E. Ary, David P. Bauer, Ian D. Bergman, Rachel M. Brunetti, Cynthia M. Chio, Shizhong A. Dai, Miles S. Dickinson, Susanna K. Elledge, Cole V. M. Helsell, Nathan L. Hendel, Emily Kang, Nadja Kern, Matvei S. Khoroshkin, Lisa L. Kirkemo, Greyson R. Lewis, Kevin Lou, Wesley M. Marin, Alison M. Maxwell, Peter F. McTigue, Douglas Myers-Turnbull, Tamas L. Nagy, Andrew M. Natale, Keely Oltion, Sergei Pourmal, Gabriel K. Reder, Nicholas J. Rettko, Peter J. Rohweder, Daniel M. C Schwarz, Sophia K. Tan, Paul V. Thomas, Ryan W. Tibble, Jason P. Town, Mary K. Tsai, Fatima S. Ugur, Douglas R. Wassarman, Alexander M. Wolff, Taia S. Wu, Derek Bogdanoff, Jennifer Li, Kurt S. Thorn, Shane O'Conchúir, Danielle L. Swaney, Eric D. Chow, Hiten D. Madhani, Sy Redding, Daniel N. Bolon, Tanja Kortemme, Joseph L. DeRisi, Martin Kampmann, James S. Fraser
Published 2018-07-01