Pesquisa | Biblioteca Virtual em Saúde

1.

OpenFold: retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization.

Ahdritz, Gustaf; Bouatta, Nazim; Floristean, Christina; Kadyan, Sachin; Xia, Qinghui; Gerecke, William; O'Donnell, Timothy J; Berenberg, Daniel; Fisk, Ian; Zanichelli, Niccolò; Zhang, Bo; Nowaczynski, Arkadiusz; Wang, Bei; Stepniewska-Dziubinska, Marta M; Zhang, Shang; Ojewole, Adegoke; Guney, Murat Efe; Biderman, Stella; Watkins, Andrew M; Ra, Stephen; Lorenzo, Pablo Ribalta; Nivon, Lucas; Weitzner, Brian; Ban, Yih-En Andrew; Chen, Shiyang; Zhang, Minjia; Li, Conglong; Song, Shuaiwen Leon; He, Yuxiong; Sorger, Peter K; Mostaque, Emad; Zhang, Zhao; Bonneau, Richard; AlQuraishi, Mohammed.

Nat Methods ; 2024 May 14.

Artigo em Inglês | MEDLINE | ID: mdl-38744917

2.

De novo design of potent and selective mimics of IL-2 and IL-15.

Silva, Daniel-Adriano; Yu, Shawn; Ulge, Umut Y; Spangler, Jamie B; Jude, Kevin M; Labão-Almeida, Carlos; Ali, Lestat R; Quijano-Rubio, Alfredo; Ruterbusch, Mikel; Leung, Isabel; Biary, Tamara; Crowley, Stephanie J; Marcos, Enrique; Walkey, Carl D; Weitzner, Brian D; Pardo-Avila, Fátima; Castellanos, Javier; Carter, Lauren; Stewart, Lance; Riddell, Stanley R; Pepper, Marion; Bernardes, Gonçalo J L; Dougan, Michael; Garcia, K Christopher; Baker, David.

Nature ; 565(7738): 186-191, 2019 01.

Artigo em Inglês | MEDLINE | ID: mdl-30626941

3.

Macromolecular modeling and design in Rosetta: recent methods and frameworks.

Leman, Julia Koehler; Weitzner, Brian D; Lewis, Steven M; Adolf-Bryfogle, Jared; Alam, Nawsad; Alford, Rebecca F; Aprahamian, Melanie; Baker, David; Barlow, Kyle A; Barth, Patrick; Basanta, Benjamin; Bender, Brian J; Blacklock, Kristin; Bonet, Jaume; Boyken, Scott E; Bradley, Phil; Bystroff, Chris; Conway, Patrick; Cooper, Seth; Correia, Bruno E; Coventry, Brian; Das, Rhiju; De Jong, René M; DiMaio, Frank; Dsilva, Lorna; Dunbrack, Roland; Ford, Alexander S; Frenz, Brandon; Fu, Darwin Y; Geniesse, Caleb; Goldschmidt, Lukasz; Gowthaman, Ragul; Gray, Jeffrey J; Gront, Dominik; Guffy, Sharon; Horowitz, Scott; Huang, Po-Ssu; Huber, Thomas; Jacobs, Tim M; Jeliazkov, Jeliazko R; Johnson, David K; Kappel, Kalli; Karanicolas, John; Khakzad, Hamed; Khar, Karen R; Khare, Sagar D; Khatib, Firas; Khramushin, Alisa; King, Indigo C; Kleffner, Robert.

Nat Methods ; 17(7): 665-680, 2020 07.

Artigo em Inglês | MEDLINE | ID: mdl-32483333

4.

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

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

PLoS Comput Biol ; 16(5): e1007507, 2020 05.

Artigo em Inglês | MEDLINE | ID: mdl-32365137

5.

RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.

Adolf-Bryfogle, Jared; Kalyuzhniy, Oleks; Kubitz, Michael; Weitzner, Brian D; Hu, Xiaozhen; Adachi, Yumiko; Schief, William R; Dunbrack, Roland L.

PLoS Comput Biol ; 14(4): e1006112, 2018 04.

Artigo em Inglês | MEDLINE | ID: mdl-29702641

6.

Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint.

Weitzner, Brian D; Gray, Jeffrey J.

J Immunol ; 198(1): 505-515, 2017 01 01.

Artigo em Inglês | MEDLINE | ID: mdl-27872211

7.

An Integrated Framework Advancing Membrane Protein Modeling and Design.

Alford, Rebecca F; Koehler Leman, Julia; Weitzner, Brian D; Duran, Amanda M; Tilley, Drew C; Elazar, Assaf; Gray, Jeffrey J.

PLoS Comput Biol ; 11(9): e1004398, 2015 Sep.

Artigo em Inglês | MEDLINE | ID: mdl-26325167

8.

Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization.

Weitzner, Brian D; Kuroda, Daisuke; Marze, Nicholas; Xu, Jianqing; Gray, Jeffrey J.

Proteins ; 82(8): 1611-23, 2014 Aug.

Artigo em Inglês | MEDLINE | ID: mdl-24519881

9.

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.

Hosseinzadeh, Parisa; Watson, Paris R; Craven, Timothy W; Li, Xinting; Rettie, Stephen; Pardo-Avila, Fátima; Bera, Asim K; Mulligan, Vikram Khipple; Lu, Peilong; Ford, Alexander S; Weitzner, Brian D; Stewart, Lance J; Moyer, Adam P; Di Piazza, Maddalena; Whalen, Joshua G; Greisen, Per Jr; Christianson, David W; Baker, David.

Nat Commun ; 12(1): 3384, 2021 06 07.

Artigo em Inglês | MEDLINE | ID: mdl-34099674

10.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design.

Le, Kathy H; Adolf-Bryfogle, Jared; Klima, Jason C; Lyskov, Sergey; Labonte, Jason; Bertolani, Steven; Burman, Shourya S Roy; Leaver-Fay, Andrew; Weitzner, Brian; Maguire, Jack; Rangan, Ramya; Adrianowycz, Matt A; Alford, Rebecca F; Adal, Aleexsan; Nance, Morgan L; Wu, Yuanhan; Willis, Jordan; Kulp, Daniel W; Das, Rhiju; Dunbrack, Roland L; Schief, William; Kuhlman, Brian; Siegel, Justin B; Gray, Jeffrey J.

Biophysicist (Rockv) ; 2(1): 108-122, 2021 Apr.

Artigo em Inglês | MEDLINE | ID: mdl-35128343

11.

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation.

Ford, Alexander S; Weitzner, Brian D; Bahl, Christopher D.

Protein Sci ; 29(1): 43-51, 2020 01.

Artigo em Inglês | MEDLINE | ID: mdl-31495995

12.

The influence of proline isomerization on potency and stability of anti-HIV antibody 10E8.

Guttman, Miklos; Padte, Neal N; Huang, Yaoxing; Yu, Jian; Rocklin, Gabriel J; Weitzner, Brian D; Scian, Michele; Ho, David D; Lee, Kelly K.

Sci Rep ; 10(1): 14313, 2020 08 31.

Artigo em Inglês | MEDLINE | ID: mdl-32868832

13.

An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases.

Weitzner, Brian; Meehan, Thomas; Xu, Qifang; Dunbrack, Roland L.

Proteins ; 75(2): 289-95, 2009 May 01.

Artigo em Inglês | MEDLINE | ID: mdl-19173308

14.

A computational method for design of connected catalytic networks in proteins.

Weitzner, Brian D; Kipnis, Yakov; Daniel, A Gerard; Hilvert, Donald; Baker, David.

Protein Sci ; 28(12): 2036-2041, 2019 12.

Artigo em Inglês | MEDLINE | ID: mdl-31642127

15.

Modeling and docking of antibody structures with Rosetta.

Weitzner, Brian D; Jeliazkov, Jeliazko R; Lyskov, Sergey; Marze, Nicholas; Kuroda, Daisuke; Frick, Rahel; Adolf-Bryfogle, Jared; Biswas, Naireeta; Dunbrack, Roland L; Gray, Jeffrey J.

Nat Protoc ; 12(2): 401-416, 2017 02.

Artigo em Inglês | MEDLINE | ID: mdl-28125104

16.

Will widgets and semantic tagging change computational biology?

Bourne, Philip E; Beran, Bojan; Bi, Chunxiao; Bluhm, Wolfgang; Dunbrack, Roland; Prlic, Andreas; Quinn, Greg; Rose, Peter; Shah, Raship; Tao, Wendy; Weitzner, Brian; Yukich, Ben.

PLoS Comput Biol ; 6(2): e1000673, 2010 Feb 26.

Artigo em Inglês | MEDLINE | ID: mdl-20195550

17.

The origin of CDR H3 structural diversity.

Weitzner, Brian D; Dunbrack, Roland L; Gray, Jeffrey J.

Structure ; 23(2): 302-11, 2015 Feb 03.

Artigo em Inglês | MEDLINE | ID: mdl-25579815

18.

A Framework to Simplify Combined Sampling Strategies in Rosetta.

Porter, Justin R; Weitzner, Brian D; Lange, Oliver F.

PLoS One ; 10(9): e0138220, 2015.

Artigo em Inglês | MEDLINE | ID: mdl-26381271

19.

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

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

PLoS One ; 8(5): e63906, 2013.

Artigo em Inglês | MEDLINE | ID: mdl-23717507

20.

I am a United Academic Worker.

Weitzner, Brian D.

Science ; 358(6360): 266, 2017 Oct 13.

Artigo em Inglês | MEDLINE | ID: mdl-29026045

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