Systematic description of COVID-19 pandemic using exact SIR solutions and Gumbel distributions von Amaro, J. E.

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Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning von Votapka, Lane W, Amaro, Rommie E

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Inclusive electron scattering within the SuSAv2 meson-exchange current approach von Megias, G. D., Amaro, J. E., Barbaro, M. B., Caballero, J. A., Donnelly, T. W.

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Modeling Energy Communities with Collective Photovoltaic Self-Consumption: Synergies between a Small City and a Winery in Portugal von Pontes Luz, Guilherme, Amaro e Silva, Rodrigo

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POVME 3.0: Software for Mapping Binding Pocket Flexibility von Wagner, Jeffrey R, Sørensen, Jesper, Hensley, Nathan, Wong, Celia, Zhu, Clare, Perison, Taylor, Amaro, Rommie E

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POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics von Durrant, Jacob D, Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E

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SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma von Andreano, Emanuele, Piccini, Giulia, Licastro, Danilo, Casalino, Lorenzo, Johnson, Nicole V., Paciello, Ida, Monego, Simeone Dal, Pantano, Elisa, Manganaro, Noemi, Manenti, Alessandro, Manna, Rachele, Casa, Elisa, Hyseni, Inesa, Benincasa, Linda, Montomoli, Emanuele, Amaro, Rommie E., McLellan, Jason S., Rappuoli, Rino

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Emerging Computational Methods for the Rational Discovery of Allosteric Drugs von Wagner, Jeffrey R, Lee, Christopher T, Durrant, Jacob D, Malmstrom, Robert D, Feher, Victoria A, Amaro, Rommie E

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A glycan gate controls opening of the SARS-CoV-2 spike protein von Sztain, Terra, Ahn, Surl-Hee, Bogetti, Anthony T., Casalino, Lorenzo, Goldsmith, Jory A., Seitz, Evan, McCool, Ryan S., Kearns, Fiona L., Acosta-Reyes, Francisco, Maji, Suvrajit, Mashayekhi, Ghoncheh, McCammon, J. Andrew, Ourmazd, Abbas, Frank, Joachim, McLellan, Jason S., Chong, Lillian T., Amaro, Rommie E.

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The flexibility of ACE2 in the context of SARS-CoV-2 infection von Barros, Emilia P., Casalino, Lorenzo, Gaieb, Zied, Dommer, Abigail C., Wang, Yuzhang, Fallon, Lucy, Raguette, Lauren, Belfon, Kellon, Simmerling, Carlos, Amaro, Rommie E.

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Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein von Casalino, Lorenzo, Gaieb, Zied, Goldsmith, Jory A, Hjorth, Christy K, Dommer, Abigail C, Harbison, Aoife M, Fogarty, Carl A, Barros, Emilia P, Taylor, Bryn C, McLellan, Jason S, Fadda, Elisa, Amaro, Rommie E

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An Integrated Markov State Model and Path Metadynamics Approach To Characterize Drug Binding Processes von Bernetti, Mattia, Masetti, Matteo, Recanatini, Maurizio, Amaro, Rommie E, Cavalli, Andrea

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Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B von Shi, Ke, Carpenter, Michael A, Banerjee, Surajit, Shaban, Nadine M, Kurahashi, Kayo, Salamango, Daniel J, McCann, Jennifer L, Starrett, Gabriel J, Duffy, Justin V, Demir, Özlem, Amaro, Rommie E, Harki, Daniel A, Harris, Reuben S, Aihara, Hideki

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SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding von Votapka, Lane W, Jagger, Benjamin R, Heyneman, Alexandra L, Amaro, Rommie E

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D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings von Gaieb, Zied, Parks, Conor D., Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Walters, W. Patrick, Lambert, Millard H., Nevins, Neysa, Bembenek, Scott D., Ameriks, Michael K., Mirzadegan, Tara, Burley, Stephen K., Amaro, Rommie E., Gilson, Michael K.

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Electron- versus neutrino-nucleus scattering von Amaro, J E, Barbaro, M B, Caballero, J A, González-Jiménez, R, Megias, G D, Simo, I Ruiz

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Axial-vector dominance predictions in quasielastic neutrino-nucleus scattering von Amaro, J. E., Ruiz Arriola, E.

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Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds von Lee, Christopher T, Comer, Jeffrey, Herndon, Conner, Leung, Nelson, Pavlova, Anna, Swift, Robert V, Tung, Chris, Rowley, Christopher N, Amaro, Rommie E, Chipot, Christophe, Wang, Yi, Gumbart, James C

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Computational approaches to mapping allosteric pathways von Feher, Victoria A, Durrant, Jacob D, Van Wart, Adam T, Amaro, Rommie E

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D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies von Gaieb, Zied, Liu, Shuai, Gathiaka, Symon, Chiu, Michael, Yang, Huanwang, Shao, Chenghua, Feher, Victoria A., Walters, W. Patrick, Kuhn, Bernd, Rudolph, Markus G., Burley, Stephen K., Gilson, Michael K., Amaro, Rommie E.

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