Large-scale application of free energy perturbation calculations for antibody design von Zhu, Fangqiang, Bourguet, Feliza A., Bennett, William F. D., Lau, Edmond Y., Arrildt, Kathryn T., Segelke, Brent W., Zemla, Adam T., Desautels, Thomas A., Faissol, Daniel M.

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Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence von Borucki, Monica K, Collette, Nicole M, Coffey, Lark L, Van Rompay, Koen K A, Hwang, Mona H, Thissen, James B, Allen, Jonathan E, Zemla, Adam T

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Single Amino Acid Mutations Affect Zika Virus Replication In Vitro and Virulence In Vivo von Collette, Nicole M, Lao, Victoria H I, Weilhammer, Dina R, Zingg, Barbara, Cohen, Shoshana D, Hwang, Mona, Coffey, Lark L, Grady, Sarah L, Zemla, Adam T, Borucki, Monica K

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Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction von Chaudhury, Sidhartha, Abdulhameed, Mohamed Diwan M, Singh, Narender, Tawa, Gregory J, D'haeseleer, Patrik M, Zemla, Adam T, Navid, Ali, Zhou, Carol E, Franklin, Matthew C, Cheung, Jonah, Rudolph, Michael J, Love, James, Graf, John F, Rozak, David A, Dankmeyer, Jennifer L, Amemiya, Kei, Daefler, Simon, Wallqvist, Anders

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StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase von Zemla, Adam T, Lang, Dorothy M, Kostova, Tanya, Andino, Raul, Ecale Zhou, Carol L

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Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types von Cadag, Eithon, Vitalis, Elizabeth, Lennox, Kristin P, Zhou, Carol L Ecale, Zemla, Adam T

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PDBspheres: a method for finding 3D similarities in local regions in proteins von Zemla, Adam T, Allen, Jonathan E, Kirshner, Dan, Lightstone, Felice C

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A Computational Pipeline to Identify and Characterize Binding Sites and Interacting Chemotypes in SARS-CoV‑2 von Sandholtz, Sarah H., Drocco, Jeffrey A., Zemla, Adam T., Torres, Marisa W., Silva, Mary S., Allen, Jonathan E.

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MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization von Zhou, Carol L Ecale, Lam, Marisa W, Smith, Jason R, Zemla, Adam T, Dyer, Matthew D, Kuczmarski, Thomas A, Vitalis, Elizabeth A, Slezak, Thomas R

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Structural re-alignment in an immunogenic surface region of ricin A chain von Zemla, Adam T, Ecale Zhou, Carol L

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Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence during in vivo passage von Peña, José, Chen-Harris, Haiyin, Allen, Jonathan E., Hwang, Mona, Elsheikh, Maher, Mabery, Shalini, Bielefeldt-Ohmann, Helle, Zemla, Adam T., Bowen, Richard A., Borucki, Monica K.

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Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin von Zhou, Carol L. Ecale, Zemla, Adam T., Roe, Diana, Young, Malin, Lam, Marisa, Schoeniger, Joseph S., Balhorn, Rod

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Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain von Zemla, Adam T., Zhou, Carol L. Ecale

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Computationally restoring the potency of a clinical antibody against Omicron von Desautels, Thomas A., Arrildt, Kathryn T., Zemla, Adam T., Lau, Edmond Y., Zhu, Fangqiang, Ricci, Dante, Cronin, Stephanie, Zost, Seth J., Binshtein, Elad, Scheaffer, Suzanne M., Dadonaite, Bernadeta, Petersen, Brenden K., Engdahl, Taylor B., Chen, Elaine, Handal, Laura S., Hall, Lynn, Goforth, John W., Vashchenko, Denis, Nguyen, Sam, Weilhammer, Dina R., Lo, Jacky Kai-Yin, Rubinfeld, Bonnee, Saada, Edwin A., Weisenberger, Tracy, Lee, Tek-Hyung, Whitener, Bradley, Case, James B., Ladd, Alexander, Silva, Mary S., Haluska, Rebecca M., Grzesiak, Emilia A., Earnhart, Christopher G., Hopkins, Svetlana, Bates, Thomas W., Thackray, Larissa B., Segelke, Brent W., Lillo, Antonietta Maria, Sundaram, Shivshankar, Bloom, Jesse D., Diamond, Michael S., Crowe, James E., Carnahan, Robert H., Faissol, Daniel M.

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Computational analysis of pathogen-borne metallo [beta]-lactamases reveals discriminating structural features between B1 types von Cadag, Eithon, Vitalis, Elizabeth, Lennox, Kristin P, Zhou, Carol L Ecale, Zemla, Adam T

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Structural Re-Alignment in an Immunogenic Surface Region of Ricin A Chain von Adam T. Zemla, Carol L. Ecale Zhou

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Rapid development of nucleic acid diagnostics von Fitch, J.P., McCready, P.M., Gardner, S.N., Kuczmarski, T.A., Kurtz, S., Myers, R., Ott, L.L., Slezak, T.R., Vitalis, E.A., Zemla, A.T.

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Rapid Countermeasure Discovery against Francisella tularensis Based on a Metabolic Network Reconstruction. e63369 von Chaudhury, Sidhartha, Abdulhameed, Mohamed DiwanM, Singh, Narender, Tawa, Gregory J, D'haeseleer, Patrik M, Zemla, Adam T, Navid, Ali, Zhou, Carol E, Franklin, Matthew C, Cheung, Jonah

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Computational approaches for identification of conserved/ unique binding dockets in the a chain of ricin von ZHOU, Carol L, ZEMLA, Adam T, ROE, Diana, YOUNG, Main, LAM, Marisa, SCHOENIGER, Joseph S, BALHORN, Rod

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REPAIRED THERAPEUTIC AND PROPHYLACTIC ANTIBODIES AGAINST SARS-COV-2 VARIANTS von DESAUTELS, Thomas Anthony, ZHU, Fangqiang, ZEMLA, Adam T, LILLO, Antonietta Maria, CARNAHAN JR., Robert Herschel, ARRILDT, Kathryn, LAU, Edmond Y, FAISSOL, Daniel M, CROWE JR., James E

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