POVME 3.0: Software for Mapping Binding Pocket Flexibility
Wagner, Jeffrey R, Sørensen, Jesper, Hensley, Nathan, Wong, Celia, Zhu, Clare, Perison, Taylor, Amaro, Rommie E
Published in Journal of chemical theory and computation (12.09.2017)
Published in Journal of chemical theory and computation (12.09.2017)
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Journal Article
POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics
Durrant, Jacob D, Votapka, Lane, Sørensen, Jesper, Amaro, Rommie E
Published in Journal of chemical theory and computation (11.11.2014)
Published in Journal of chemical theory and computation (11.11.2014)
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Journal Article
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
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
Published in Proceedings of the National Academy of Sciences - PNAS (07.09.2021)
Published in Proceedings of the National Academy of Sciences - PNAS (07.09.2021)
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Journal Article
A glycan gate controls opening of the SARS-CoV-2 spike protein
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.
Published in Nature chemistry (01.10.2021)
Published in Nature chemistry (01.10.2021)
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Journal Article
The flexibility of ACE2 in the context of SARS-CoV-2 infection
Barros, Emilia P., Casalino, Lorenzo, Gaieb, Zied, Dommer, Abigail C., Wang, Yuzhang, Fallon, Lucy, Raguette, Lauren, Belfon, Kellon, Simmerling, Carlos, Amaro, Rommie E.
Published in Biophysical journal (16.03.2021)
Published in Biophysical journal (16.03.2021)
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Journal Article
Beyond Shielding: The Roles of Glycans in the SARS-CoV‑2 Spike Protein
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
Published in ACS central science (28.10.2020)
Published in ACS central science (28.10.2020)
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Journal Article
Emerging Computational Methods for the Rational Discovery of Allosteric Drugs
Wagner, Jeffrey R, Lee, Christopher T, Durrant, Jacob D, Malmstrom, Robert D, Feher, Victoria A, Amaro, Rommie E
Published in Chemical reviews (08.06.2016)
Published in Chemical reviews (08.06.2016)
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Journal Article
SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin–Benzamidine Binding
Votapka, Lane W, Jagger, Benjamin R, Heyneman, Alexandra L, Amaro, Rommie E
Published in The journal of physical chemistry. B (20.04.2017)
Published in The journal of physical chemistry. B (20.04.2017)
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Journal Article
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
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
Published in Journal of chemical information and modeling (25.04.2016)
Published in Journal of chemical information and modeling (25.04.2016)
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Journal Article
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
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
Published in Nature structural & molecular biology (01.02.2017)
Published in Nature structural & molecular biology (01.02.2017)
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Journal Article
Computational approaches to mapping allosteric pathways
Feher, Victoria A, Durrant, Jacob D, Van Wart, Adam T, Amaro, Rommie E
Published in Current opinion in structural biology (01.04.2014)
Published in Current opinion in structural biology (01.04.2014)
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Journal Article
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
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.
Published in Journal of computer-aided molecular design (01.01.2018)
Published in Journal of computer-aided molecular design (01.01.2018)
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Journal Article
Markov state models and NMR uncover an overlooked allosteric loop in p53
Barros, Emilia P, Demir, Özlem, Soto, Jenaro, Cocco, Melanie J, Amaro, Rommie E
Published in Chemical science (Cambridge) (16.12.2020)
Published in Chemical science (Cambridge) (16.12.2020)
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Journal Article
D3R grand challenge 2015: Evaluation of protein–ligand pose and affinity predictions
Gathiaka, Symon, Liu, Shuai, Chiu, Michael, Yang, Huanwang, Stuckey, Jeanne A., Kang, You Na, Delproposto, Jim, Kubish, Ginger, Dunbar, James B., Carlson, Heather A., Burley, Stephen K., Walters, W. Patrick, Amaro, Rommie E., Feher, Victoria A., Gilson, Michael K.
Published in Journal of computer-aided molecular design (01.09.2016)
Published in Journal of computer-aided molecular design (01.09.2016)
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Journal Article
Two Relations to Estimate Membrane Permeability Using Milestoning
Votapka, Lane W, Lee, Christopher T, Amaro, Rommie E
Published in The journal of physical chemistry. B (25.08.2016)
Published in The journal of physical chemistry. B (25.08.2016)
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Journal Article
D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings
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.
Published in Journal of computer-aided molecular design (01.01.2019)
Published in Journal of computer-aided molecular design (01.01.2019)
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