Publications

Glycan masking in vaccine design: Targets, immunogens and applications.

Martina CE, Crowe JE Jr, Meiler J.

Front Immunol. 2023 Mar 23;14:1126034. doi: 10.3389/fimmu.2023.1126034. eCollection 2023.
Antigenic mapping and functional characterization of human New World hantavirus neutralizing antibodies.

Engdahl TB, Binshtein E, Brocato RL, Kuzmina NA, Principe LM, Kwilas SA, Kim RK, Chapman NS, Porter MS, Guardado-Calvo P, Rey FA, Handal LS, Diaz SM, Zagol-Ikapitte IA, Tran MH, McDonald WH, Meiler J, Reidy JX, Trivette A, Bukreyev A, Hooper JW, Crowe JE.

Elife. 2023 Mar 27;12:e81743. doi: 10.7554/eLife.81743.

Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals.

Bozhanova NG, Flyak AI, Brown BP, Ruiz SE, Salas J, Rho S, Bombardi RG, Myers L, Soto C, Bailey JR, Crowe JE Jr, Bjorkman PJ, Meiler J.

Nat Commun. 2022 Jun 8;13(1):3178. doi: 10.1038/s41467-022-30865-9.
Therapeutic alphavirus cross-reactive E1 human antibodies inhibit viral egress.

Williamson LE, Reeder KM, Bailey K, Tran MH, Roy V, Fouch ME, Kose N, Trivette A, Nargi RS, Winkler ES, Kim AS, Gainza C, Rodriguez J, Armstrong E, Sutton RE, Reidy J, Carnahan RH, McDonald WH, Schoeder CT, Klimstra WB, Davidson E, Doranz BJ, Alter G, Meiler J, Schey KL, Julander JG, Diamond MS, Crowe JE Jr.

Cell. 2021 Aug 19;184(17):4430-4446.e22. doi: 10.1016/j.cell.2021.07.033.
Epitope-focused immunogen design based on the ebolavirus glycoprotein HR2-MPER region.

Schoeder CT, Gilchuk P, Sangha AK, Ledwitch KV, Malherbe DC, Zhang X, Binshtein E, Williamson LE, Martina CE, Dong J, Armstrong E, Sutton R, Nargi R, Rodriguez J, Kuzmina N, Fiala B, King NP, Bukreyev A, Crowe JE Jr, Meiler J.

PLoS Pathog. 2022 May 18;18(5):e1010518. doi: 10.1371/journal.ppat.1010518. eCollection 2022 May.
Potently neutralizing and protective human antibodies against SARS-CoV-2.

Zost SJ, Gilchuk P, Case JB, Binshtein E, Chen RE, Nkolola JP, Schäfer A, Reidy JX, Trivette A, Nargi RS, Sutton RE, Suryadevara N, Martinez DR, Williamson LE, Chen EC, Jones T, Day S, Myers L, Hassan AO, Kafai NM, Winkler ES, Fox JM, Shrihari S, Mueller BK, Meiler J, Chandrashekar A, Mercado NB, Steinhardt JJ, Ren K, Loo YM, Kallewaard NL, McCune BT, Keeler SP, Holtzman MJ, Barouch DH, Gralinski LE, Baric RS, Thackray LB, Diamond MS, Carnahan RH, Crowe JE Jr.

Nature. 2020 Aug;584(7821):443-449. doi: 10.1038/s41586-020-2548-6. Epub 2020 Jul 15.
Integrating linear optimization with structural modeling to increase HIV neutralization breadth.

Sevy AM, Panda S, Crowe JE Jr, Meiler J, Vorobeychik Y.

PLoS Comput Biol. 2018 Feb 16;14(2):e1005999. doi: 10.1371/journal.pcbi.1005999. eCollection 2018 Feb.
Computationally Designed Cyclic Peptides Derived from an Antibody Loop Increase Breadth of Binding for Influenza Variants.

Sevy AM, Gilchuk IM, Brown BP, Bozhanova NG, Nargi R, Jensen M, Meiler J, Crowe JE Jr.

Structure. 2020 Oct 6;28(10):1114-1123.e4. doi: 10.1016/j.str.2020.04.005. Epub 2020 Jun 30.
Multi-state design of flexible proteins predicts sequences optimal for conformational change.

Sauer MF, Sevy AM, Crowe JE Jr, Meiler J.

PLoS Comput Biol. 2020 Feb 7;16(2):e1007339. doi: 10.1371/journal.pcbi.1007339. eCollection 2020 Feb.
The human antibody sequence space and structural design of the V, J regions, and CDRH3 with Rosetta.

Schmitz S, Schmitz EA, Crowe JE Jr, Meiler J.

MAbs. 2022 Jan-Dec;14(1):2068212. doi: 10.1080/19420862.2022.2068212.
Identification of Structurally Related Antibodies in Antibody Sequence Databases Using Rosetta-Derived Position-Specific Scoring.

Finn JA, Dong J, Sevy AM, Parrish E, Gilchuk I, Nargi R, Scarlett-Jones M, Reichard W, Bombardi R, Voss TG, Meiler J, Crowe JE Jr.

Structure. 2020 Oct 6;28(10):1124-1130.e5. doi: 10.1016/j.str.2020.07.012. Epub 2020 Aug 11.
RosettaCM for antibodies with very long HCDR3s and low template availability.

Kodali P, Schoeder CT, Schmitz S, Crowe JE , Jr, Meiler J.

Proteins. 2021 Nov;89(11):1458-1472. doi: 10.1002/prot.26166. Epub 2021 Jul 7.
Computational epitope mapping of class I fusion proteins using low complexity supervised learning methods.

Fischer MFS, Crowe JE, Meiler J.

PLoS Comput Biol. 2022 Dec 7;18(12):e1010230. doi: 10.1371/journal.pcbi.1010230. eCollection 2022 Dec.
Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.

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, Bender BJ, Martina CE, Del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE Jr, Meiler J, Moretti R.

Biochemistry. 2021 Mar 23;60(11):825-846. doi: 10.1021/acs.biochem.0c00912. Epub 2021 Mar 11.
Improving Loop Modeling of the Antibody Complementarity-Determining Region 3 Using Knowledge-Based Restraints. Finn JA, Koehler Leman J, Willis JR, Cisneros A 3rd, Crowe JE Jr, Meiler J. PLoS One. 2016 May 16.
Long Antibody HCDR3s from HIV-naive donors presented on a PG9 neutralizing antibody background mediate HIV neutralization. Willis JR, Finn JA, Briney B, Sapparapu G, Singh V, King H, LaBranche CC, Montefiori DC, Meiler J, Crowe JE Jr. PNAS. 2016 April 19.
Vaccine-elicited antibody that neutralizes H5N1 influenza and variants binds the receptor site and polymorphic sites. Winarski KL, Thornburg NJ, Yu Y, Sapparapu G, Crowe JE Jr., Spiller BW. PNAS. 2015 July 28.
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences. Sevy AM, Jacobs TM, Crowe JE Jr, Meiler J. PLoS Computational Biology. 2015 July 6.
Redesigned HIV antibodies exhibit enhanced neutralizing potency and breadth. Willis JR, Sapparapu G, Murrell S, Julien JP, Singh V, King HG, Xia Y, Pickens JA, LaBranche CC, Slaughter JC, Montefiori DC, Wilson IA, Meiler J, Crowe JE Jr. Journal of Clinical Investigation. 2015 June.
Differential accessibility of a rotavirus VP6 epitope in trimers comprising type I, II, or III channels as revealed by binding of a human rotavirus VP6-specific antibody. Aiyegbo MS, Eli IM, Spiller BW, Williams DR, Kim R, Lee DE, Liu T, Li S, Stewart PL, Crowe JE Jr. Journal of Virology. 2014 Jan.

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