Sampling of structure and sequence space of small protein folds

Autor: Thomas W. Linsky, Kyle Noble, Autumn R. Tobin, Rachel Crow, Lauren Carter, Jeffrey L. Urbauer, David Baker, Eva-Maria Strauch

Publikováno v: Nature Communications, Vol 13, Iss 1, Pp 1-11 (2022)

In this work the authors provide a computational workflow for the parallel, from scratch, design of proteins to rapidly explore the shape diversity of protein folds.

Externí odkaz: https://doaj.org/article/9e18f64e63334c078ec04aa56a87a687

Sampling of Structure and Sequence Space of Small Protein Folds

Autor: Lauren Carter, K. Noble, David Baker, Thomas W. Linsky, J. L. Urbauer, R. Crow, Eva-Maria Strauch, A. Tobin

Nature only samples a small fraction in sequence space, yet many more amino acid combinations can fold into stable proteins. Furthermore, small structural variations in a single fold, which may only be a few amino acids different from the next homolo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::940b55035ed95f96edbaac02dd741033
https://doi.org/10.1101/2021.03.10.434454

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Autor: Jack Maguire, Ragul Gowthaman, Marion F. Sauer, Georg Kuenze, Tanja Kortemme, Benjamin Basanta, Indigo Chris King, Jens Meiler, Rhiju Das, Ora Schueler-Furman, Nicholas A. Marze, Brandon Frenz, Christoffer Norn, Julia Koehler Leman, Jason W. Labonte, Kala Bharath Pilla, Lei Shi, Sergey Lyskov, Brian D. Weitzner, Nir London, Karen R. Khar, Jaume Bonet, Nawsad Alam, Andreas Scheck, Alexander M. Sevy, Lars Malmström, Thomas Huber, Christopher Bystroff, Lior Zimmerman, Lorna Dsilva, Bruno E. Correia, Roland L. Dunbrack, Sergey Ovchinnikov, Rocco Moretti, Scott Horowitz, Phil Bradley, Frank DiMaio, Noah Ollikainen, Brian Kuhlman, Jeffrey J. Gray, Melanie L. Aprahamian, Andrew Leaver-Fay, Santrupti Nerli, Brian Koepnick, Xingjie Pan, Manasi A. Pethe, Andrew M. Watkins, Summer B. Thyme, Enrique Marcos, Vikram Khipple Mulligan, Hahnbeom Park, Po-Ssu Huang, David K. Johnson, Daniel-Adriano Silva, Patrick Barth, Shannon Smith, Caleb Geniesse, Jason K. Lai, Patrick Conway, Amelie Stein, Jeliazko R. Jeliazkov, David Baker, Dominik Gront, Kalli Kappel, Firas Khatib, Robert Kleffner, Brian J. Bender, Richard Bonneau, Kyle A. Barlow, Joseph H. Lubin, Shourya S. Roy Burman, Nikolaos G. Sgourakis, Yuval Sedan, Ryan E. Pavlovicz, Kristin Blacklock, Seth Cooper, Barak Raveh, Alisa Khramushin, John Karanicolas, Justin B. Siegel, Sharon L. Guffy, Brian G. Pierce, Alex Ford, Darwin Y. Fu, Orly Marcu, Gideon Lapidoth, Brian Coventry, René M. de Jong, Shane O’Conchúir, Thomas W. Linsky, William R. Schief, Rebecca F. Alford, Scott E. Boyken, Sagar D. Khare, Maria Szegedy, Ray Yu-Ruei Wang, Steven M. Lewis, Hamed Khakzad, Timothy M. Jacobs, Frank D. Teets, Lukasz Goldschmidt, Daisuke Kuroda, Steffen Lindert, P. Douglas Renfrew, Yifan Song, Jared Adolf-Bryfogle, Michael S. Pacella, Aliza B. Rubenstein

Publikováno v: Nat Methods

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactore

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c561276e840d68005d2aab06fb9642da
https://pubmed.ncbi.nlm.nih.gov/32483333

Discovery of structurally-diverse inhibitor scaffolds by high-throughput screening of a fragment library with dimethylarginine dimethylaminohydrolase

Autor: Walter Fast, Thomas W. Linsky

Publikováno v: Bioorganic & Medicinal Chemistry. 20:5550-5558

Potent and selective inhibitors of the enzyme dimethylarginine dimethylaminohydrolase (DDAH) are useful as molecular probes to better understand cellular regulation of nitric oxide. Inhibitors are also potential therapeutic agents for treatment of pa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c084841931b4363904c5694a69f21ff6
https://doi.org/10.1016/j.bmc.2012.07.022

On the Mechanism of Dimethylarginine Dimethylaminohydrolase Inactivation by 4-Halopyridines

Autor: Corey M. Johnson, Zhihong Ke, Arthur F. Monzingo, Walter Fast, Hua Guo, Jon D. Robertus, Thomas W. Linsky, Dae Wi Yoon

Publikováno v: Journal of the American Chemical Society. 133:10951-10959

Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa33c1bd46a400c327abd054d4abab15
https://doi.org/10.1021/ja2033684