Amaro, Rommie E.

D3R grand challenge 2015: evaluation of protein-ligand pose and affinity predictions.

Gathiaka, S., Liu, S., Chiu, M., Yang, H., Stuckey, J. A., Kang, Y. N., Delproposto, J., Kubish, G., Dunbar, J. B., Carlson, H. A., et al. (2016) · Journal of Computer-Aided Molecular Design

Computational Drug Discovery MethodsProtein Structure and Dynamics

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A critical overview of computational approaches employed for COVID-19 drug discovery

Muratov, E. N., Amaro, R., Andrade, C. H., Brown, N., Ekins, S., Fourches, D., Isayev, O., Kozakov, D., Medina-Franco, J. L., Merz, K. M., et al. (2021) · Chemical Society Reviews

Computational Drug Discovery MethodsSARS-CoV-2 and COVID-19 Research

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D3R grand challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies.

Gaieb, Z., Liu, S., Gathiaka, S., Chiu, M., Yang, H., Shao, C., Feher, V. A., Walters, W. P., Kuhn, B., Rudolph, M. G., et al. (2018) · Journal of Computer-Aided Molecular Design

Computational Drug Discovery MethodsProtein Structure and Dynamics

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CACHE (Critical Assessment of Computational Hit-finding Experiments): A public–private partnership benchmarking initiative to enable the development of computational methods for hit-finding

Ackloo, S., Al-awar, R., Amaro, R. E., Arrowsmith, C. H., Azevedo, H., Batey, R. A., Bengio, Y., Betz, U. A. K., Bologa, C. G., Chodera, J. D., et al. (2022) · Nature Reviews Chemistry

Computational Drug Discovery MethodsProtein Degradation and Inhibitors

Cited by 112

Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE

Chongsaritsinsuk, J., Steigmeyer, A. D., Mahoney, K. E., Rosenfeld, M. A., Lucas, T. M., Smith, C. M., Li, A., Ince, D., Kearns, F. L., Battison, A. S., et al. (2023) · Nature Communications

Glycosylation and Glycoproteins ResearchCarbohydrate Chemistry and Synthesis

Cited by 52

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamic and kinetic sampling

Ahn, S.-H., Ojha, A., Amaro, R., & McCammon, J. (2021) · Journal of Chemical Theory and Computation

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 40

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamics and kinetics sampling

Ahn, S.-H., Ojha, A., Amaro, R., & McCammon, J. (2021) · Journal of Chemical Theory and Computation

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 40

QMrebind: incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Ojha, A. A., Votapka, L. W., & Amaro, R. E. (2023) · Chemical Science

Computational Drug Discovery MethodsProtein Structure and Dynamics

Cited by 19

Distinct pathway for evolution of enhanced receptor binding and cell entry in SARS-like bat coronaviruses

Tse, A. L., Acreman, C. M., Ricardo-Lax, I., Berrigan, J., Lasso, G., Balogun, T., Kearns, F. L., Casalino, L., McClain, G. L., Chandran, A. M., et al. (2024) · PLoS Pathogens

SARS-CoV-2 and COVID-19 ResearchAnimal Virus Infections Studies

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Regulatory Interactions between APOBEC3B N- and C-Terminal Domains

Braza, M. K. E., Demir, Ö., Ahn, S.-H., Morris, C. K., Calvó-Tusell, C., McGuire, K. L., de la Peña Avalos, B., Carpenter, M. A., Chen, Y., Casalino, L., et al. (2025) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 3

Markovian state models uncover casein kinase 1 dynamics that govern circadian period

Ricci, C. G., Philpott, J. M., Torgrimson, M. R., Freeberg, A. M., Narasimamurthy, R., Pécora de Barros, E., Amaro, R., Virshup, D. M., McCammon, J. A., & Partch, C. L. (2025) · Biophysical Journal

Circadian rhythm and melatoninProtein Structure and Dynamics

Cited by 3

Regulatory interactions between APOBEC3B N- and C-terminal domains

Braza, M. K. E., Demir, Ö., Ahn, S.-H., Morris, C. K., Calvó-Tusell, C., McGuire, K. L., de la Peña Avalos, B., Carpenter, M. A., Chen, Y., Casalino, L., et al. (2024) · Journal of Chemical Information and Modeling

Protein Structure and DynamicsEnzyme Structure and Function

Cited by 3

Markovian State Models uncover Casein Kinase 1 dynamics that govern circadian period

Ricci, C. G., Philpott, J. M., Torgrimson, M. R., Freeberg, A. M., Narasimamurthy, R., Pécora de Barros, E., Amaro, R., Virshup, D. M., McCammon, J. A., & Partch, C. L. (2025) · Biophysical Journal

Circadian rhythm and melatoninProtein Structure and Dynamics

Cited by 3

Gaussian accelerated molecular dynamics with the weighted ensemble method: a hybrid method improves thermodynamics and kinetics sampling

Ahn, S.-H., Ojha, A., Amaro, R., & McCammon, J. (2021)

Advanced Physical and Chemical Molecular InteractionsProtein Structure and Dynamics

Cited by 1

Structural dynamics and allosteric communication of a SARS-like bat coronavirus spike glycoprotein

Balogun, T. A., Kearns, F. L., Calvó-Tusell, C., Tse, A. L., Acreman, C. M., Casalino, L., Lasso, G., Miller, E. H., Chandran, K., McLellan, J. S., et al. (2026) · Biophysical Journal

SARS-CoV-2 and COVID-19 ResearchProtein Structure and Dynamics

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