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Brian Weitzner - Publications

Affiliations: 
2015 Chemical & Biomolecular Engineering Johns Hopkins University, Baltimore, MD 
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18 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147  0.737
2021 Hosseinzadeh P, Watson PR, Craven TW, Li X, Rettie S, Pardo-Avila F, Bera AK, Mulligan VK, Lu P, Ford AS, Weitzner BD, Stewart LJ, Moyer AP, Di Piazza M, Whalen JG, et al. Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Nature Communications. 12: 3384. PMID 34099674 DOI: 10.1038/s41467-021-23609-8  0.355
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.653
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.709
2019 Weitzner BD, Kipnis Y, Daniel AG, Hilvert D, Baker D. A computational method for design of connected catalytic networks in proteins. Protein Science : a Publication of the Protein Society. PMID 31642127 DOI: 10.1002/Pro.3757  0.302
2019 Ford AS, Weitzner BD, Bahl CD. Integration of the Rosetta Suite with the Python Software Stack via reproducible packaging and core programming interfaces for distributed simulation. Protein Science : a Publication of the Protein Society. PMID 31495995 DOI: 10.1002/Pro.3721  0.334
2018 Adolf-Bryfogle J, Kalyuzhniy O, Kubitz M, Weitzner BD, Hu X, Adachi Y, Schief WR, Dunbrack RL. RosettaAntibodyDesign (RAbD): A general framework for computational antibody design. Plos Computational Biology. 14: e1006112. PMID 29702641 DOI: 10.1371/Journal.Pcbi.1006112  0.737
2017 Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nature Protocols. 12: 401-416. PMID 28125104 DOI: 10.1038/Nprot.2016.180  0.735
2016 Weitzner BD, Gray JJ. Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint. Journal of Immunology (Baltimore, Md. : 1950). PMID 27872211 DOI: 10.4049/Jimmunol.1601137  0.564
2015 Porter JR, Weitzner BD, Lange OF. A Framework to Simplify Combined Sampling Strategies in Rosetta. Plos One. 10: e0138220. PMID 26381271 DOI: 10.1371/journal.pone.0138220  0.313
2015 Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray JJ. An Integrated Framework Advancing Membrane Protein Modeling and Design. Plos Computational Biology. 11: e1004398. PMID 26325167 DOI: 10.1371/Journal.Pcbi.1004398  0.525
2015 Weitzner BD, Dunbrack RL, Gray JJ. The origin of CDR H3 structural diversity. Structure (London, England : 1993). 23: 302-11. PMID 25579815 DOI: 10.1016/J.Str.2014.11.010  0.652
2014 Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ. Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins. 82: 1611-23. PMID 24519881 DOI: 10.1002/Prot.24534  0.684
2013 Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/Journal.Pone.0063906  0.714
2011 Baugh EH, Lyskov S, Weitzner BD, Gray JJ. Real-time PyMOL visualization for Rosetta and PyRosetta Plos One. 6. PMID 21857909 DOI: 10.1371/Journal.Pone.0021931  0.519
2011 Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, Gray JJ. Benchmarking and analysis of protein docking performance in Rosetta v3.2. Plos One. 6: e22477. PMID 21829626 DOI: 10.1371/Journal.Pone.0022477  0.694
2010 Bourne PE, Beran B, Bi C, Bluhm W, Dunbrack R, Prlić A, Quinn G, Rose P, Shah R, Tao W, Weitzner B, Yukich B. Will widgets and semantic tagging change computational biology? Plos Computational Biology. 6: e1000673. PMID 20195550 DOI: 10.1371/Journal.Pcbi.1000673  0.547
2009 Weitzner B, Meehan T, Xu Q, Dunbrack RL. An unusually small dimer interface is observed in all available crystal structures of cytosolic sulfotransferases. Proteins. 75: 289-95. PMID 19173308 DOI: 10.1002/Prot.22347  0.631
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