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Rommie E. Amaro
Rommie E. Amaro
Distinguished Professorship in Theoretical and Computational Chemistry, UC San Diego.
Verified email at ucsd.edu - Homepage
Title
Cited by
Cited by
Year
Beyond shielding: the roles of glycans in the SARS-CoV-2 spike protein
L Casalino, Z Gaieb, JA Goldsmith, CK Hjorth, AC Dommer, AM Harbison, ...
ACS central science 6 (10), 1722-1734, 2020
8122020
Ensemble docking in drug discovery
RE Amaro, J Baudry, J Chodera, Ö Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
3892018
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
RE Amaro, R Baron, JA McCammon
Journal of computer-aided molecular design 22, 693-705, 2008
3852008
A glycan gate controls opening of the SARS-CoV-2 spike protein
T Sztain, SH Ahn, AT Bogetti, L Casalino, JA Goldsmith, E Seitz, ...
Nature chemistry 13 (10), 963-968, 2021
2822021
SARS-CoV-2 escape in vitro from a highly neutralizing COVID-19 convalescent plasma
E Andreano, G Piccini, D Licastro, L Casalino, NV Johnson, I Paciello, ...
BioRxiv, 2020
2792020
Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B
K Shi, MA Carpenter, S Banerjee, NM Shaban, K Kurahashi, ...
Nature structural & molecular biology 24 (2), 131-139, 2017
2532017
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
LS Cheng, RE Amaro, D Xu, WW Li, PW Arzberger, JA McCammon
Journal of medicinal chemistry 51 (13), 3878-3894, 2008
2432008
POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics
JD Durrant, L Votapka, J Sřrensen, RE Amaro
Journal of chemical theory and computation 10 (11), 5047-5056, 2014
2342014
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
CD Wassman, R Baronio, Ö Demir, BD Wallentine, CK Chen, LV Hall, ...
Nature communications 4 (1), 1407, 2013
2332013
Emerging computational methods for the rational discovery of allosteric drugs
JR Wagner, CT Lee, JD Durrant, RD Malmstrom, VA Feher, RE Amaro
Chemical reviews 116 (11), 6370-6390, 2016
2162016
D3R grand challenge 2015: evaluation of protein–ligand pose and affinity predictions
S Gathiaka, S Liu, M Chiu, H Yang, JA Stuckey, YN Kang, J Delproposto, ...
Journal of computer-aided molecular design 30, 651-668, 2016
2112016
Simulation-based approaches for determining membrane permeability of small compounds
CT Lee, J Comer, C Herndon, N Leung, A Pavlova, RV Swift, C Tung, ...
Journal of chemical information and modeling 56 (4), 721-733, 2016
2102016
SARS-CoV-2 escape from a highly neutralizing COVID-19 convalescent plasma
E Andreano, G Piccini, D Licastro, L Casalino, NV Johnson, I Paciello, ...
Proceedings of the National Academy of Sciences 118 (36), e2103154118, 2021
2092021
D3R Grand Challenge 2: blind prediction of protein–ligand poses, affinity rankings, and relative binding free energies
Z Gaieb, S Liu, S Gathiaka, M Chiu, H Yang, C Shao, VA Feher, ...
Journal of computer-aided molecular design 32, 1-20, 2018
1962018
POVME 3.0: software for mapping binding pocket flexibility
JR Wagner, J Sřrensen, N Hensley, C Wong, C Zhu, T Perison, ...
Journal of chemical theory and computation 13 (9), 4584-4592, 2017
1872017
Remarkable loop flexibility in avian influenza N1 and its implications for antiviral drug design
RE Amaro, DDL Minh, LS Cheng, WM Lindstrom, AJ Olson, JH Lin, WW Li, ...
Journal of the American Chemical Society 129 (25), 7764-7765, 2007
1832007
Exploring residue component contributions to dynamical network models of allostery
AT VanWart, J Eargle, Z Luthey-Schulten, RE Amaro
Journal of chemical theory and computation 8 (8), 2949-2961, 2012
1772012
Weighted implementation of suboptimal paths (WISP): an optimized algorithm and tool for dynamical network analysis
AT Van Wart, J Durrant, L Votapka, RE Amaro
Journal of chemical theory and computation 10 (2), 511-517, 2014
1702014
A critical overview of computational approaches employed for COVID-19 drug discovery
EN Muratov, R Amaro, CH Andrade, N Brown, S Ekins, D Fourches, ...
Chemical Society Reviews 50 (16), 9121-9151, 2021
1582021
A multiscale coarse-grained model of the SARS-CoV-2 virion
A Yu, AJ Pak, P He, V Monje-Galvan, L Casalino, Z Gaieb, AC Dommer, ...
Biophysical journal 120 (6), 1097-1104, 2021
1562021
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