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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
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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
4232020
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 (9), 693-705, 2008
3562008
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
2572020
Ensemble docking in drug discovery
RE Amaro, J Baudry, J Chodera, ÷ Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
2562018
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
2352008
Computational identification of a transiently open L1/S3 pocket for reactivation of mutant p53
CD Wassman, R Baronio, ÷ Demir, BD Wallentine, CK Chen, LV Hall, ...
Nature communications 4 (1), 1-9, 2013
1972013
POVME 2.0: an enhanced tool for determining pocket shape and volume characteristics
JD Durrant, L Votapka, J SÝrensen, RE Amaro
Journal of chemical theory and computation 10 (11), 5047-5056, 2014
1932014
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
1842017
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 (9), 651-668, 2016
1762016
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
1732016
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
1692007
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
1592016
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), 1-20, 2018
1582018
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
1572012
Characterizing loop dynamics and ligand recognition in human-and avian-type influenza neuraminidases via generalized born molecular dynamics and end-point free energy calculations
RE Amaro, X Cheng, I Ivanov, D Xu, JA McCammon
Journal of the American Chemical Society 131 (13), 4702-4709, 2009
1412009
Mechanism of 150-cavity formation in influenza neuraminidase
RE Amaro, RV Swift, L Votapka, WW Li, RC Walker, RM Bush
Nature communications 2 (1), 1-7, 2011
1362011
Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei
RE Amaro, A Schnaufer, H Interthal, W Hol, KD Stuart, JA McCammon
Proceedings of the National Academy of Sciences 105 (45), 17278-17283, 2008
1342008
Computational approaches to mapping allosteric pathways
VA Feher, JD Durrant, AT Van Wart, RE Amaro
Current opinion in structural biology 25, 98-103, 2014
1272014
POVME 3.0: software for mapping binding pocket flexibility
JR Wagner, J SÝrensen, N Hensley, C Wong, C Zhu, T Perison, ...
Journal of chemical theory and computation 13 (9), 4584-4592, 2017
1202017
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
1202014
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