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Jared Adolf-Bryfogle - Publications

Affiliations: 
2020- Institute for Protein Innovation 
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28 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
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Corrigendum to "Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus" [Heliyon 9(4) (April 2023) e15032]. Heliyon. 9: e17901. PMID 37701412 DOI: 10.1016/j.heliyon.2023.e17901  0.54
2023 Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus. Heliyon. 9: e15032. PMID 37035348 DOI: 10.1016/j.heliyon.2023.e15032  0.566
2022 Colom MS, Vucinic J, Adolf-Bryfogle J, Bowman JW, Verel S, Moczygemba I, Schiex T, Simoncini D, Bahl CD. Deep Evolutionary Forecasting identifies highly-mutated SARS-CoV-2 variants via functional sequence-landscape enumeration. Research Square. PMID 36482980 DOI: 10.21203/rs.3.rs-2248327/v1  0.652
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  0.754
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  0.756
2021 Taher NM, Hvorecny KL, Burke CM, Gilman MSA, Heussler GE, Adolf-Bryfogle J, Bahl CD, O'Toole GA, Madden DR. Biochemical and structural characterization of two cif-like epoxide hydrolases from . Current Research in Structural Biology. 3: 72-84. PMID 34235487 DOI: 10.1016/j.crstbi.2021.02.002  0.66
2021 Schoeder CT, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, et al. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry. PMID 33705117 DOI: 10.1021/acs.biochem.0c00912  0.602
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte JW, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner BD, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design The Biophysicist. 2: 108-122. DOI: 10.35459/TBP.2019.000147  0.59
2020 Adolf-Bryfogle J, Teets FD, Bahl CD. Toward complete rational control over protein structure and function through computational design. Current Opinion in Structural Biology. 66: 170-177. PMID 33276237 DOI: 10.1016/j.sbi.2020.10.015  0.67
2020 Kelow SP, Adolf-Bryfogle J, Dunbrack RL. Hiding in plain sight: structure and sequence analysis reveals the importance of the antibody DE loop for antibody-antigen binding. Mabs. 12: 1840005. PMID 33180672 DOI: 10.1080/19420862.2020.1840005  0.543
2020 Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: a database of high resolution coronavirus protein structures. Nucleic Acids Research. PMID 32890396 DOI: 10.1093/Nar/Gkaa731  0.623
2020 Gowthaman R, Guest JD, Yin R, Adolf-Bryfogle J, Schief WR, Pierce BG. CoV3D: A database of high resolution coronavirus protein structures. Biorxiv : the Preprint Server For Biology. PMID 32577656 DOI: 10.1101/2020.05.12.091983  0.552
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  0.75
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  0.744
2020 Leman JK, 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, Schueler-Furman O, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.623
2020 Leman JK, 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, Schueler-Furman O, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.647
2020 Leman JK, 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, Schueler-Furman O, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.633
2020 Leman JK, 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, Schueler-Furman O, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.606
2020 Leman JK, 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, Schueler-Furman O, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.622
2020 Leman JK, 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, Schueler-Furman O, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003  0.663
2020 Leman JK, 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, Schueler-Furman O, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.636
2020 Leman JK, 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, Schueler-Furman O, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.609
2018 Frenz B, Rämisch S, Borst AJ, Walls AC, Adolf-Bryfogle J, Schief WR, Veesler D, DiMaio F. Automatically Fixing Errors in Glycoprotein Structures with Rosetta. Structure (London, England : 1993). PMID 30344107 DOI: 10.1016/J.Str.2018.09.006  0.568
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  0.75
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  0.76
2016 Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ. Residue-centric modeling and design of saccharide and glycoconjugate structures. Journal of Computational Chemistry. PMID 27900782 DOI: 10.1002/Jcc.24679  0.635
2015 Adolf-Bryfogle J, Xu Q, North B, Lehmann A, Dunbrack RL. PyIgClassify: a database of antibody CDR structural classifications. Nucleic Acids Research. 43: D432-8. PMID 25392411 DOI: 10.1093/Nar/Gku1106  0.677
2013 Adolf-Bryfogle J, Dunbrack RL. The PyRosetta Toolkit: a graphical user interface for the Rosetta software suite. Plos One. 8: e66856. PMID 23874400 DOI: 10.1371/Journal.Pone.0066856  0.604
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