Rommie E. Amaro
Rommie E. Amaro
Professor and Shuler Scholar, Chemistry and Biochemistry, University of California, San Diego
Verified email at ucsd.edu - Homepage
Title
Cited by
Cited by
Year
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
3142008
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
2162008
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
1622007
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
1532013
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
1362014
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
1282009
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
1242016
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
1242012
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
1222011
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, 2017
1212017
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
1192008
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
1152016
Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble
MR Landon, RE Amaro, R Baron, CH Ngan, D Ozonoff, ...
Chemical biology & drug design 71 (2), 106-116, 2008
1112008
Emerging methods for ensemble-based virtual screening
RE Amaro, WW Li
Current topics in medicinal chemistry 10 (1), 3-13, 2010
1082010
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
1072016
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
1052018
Computational approaches to mapping allosteric pathways
VA Feher, JD Durrant, AT Van Wart, RE Amaro
Current opinion in structural biology 25, 98-103, 2014
972014
A multidimensional strategy to detect polypharmacological targets in the absence of structural and sequence homology
JD Durrant, RE Amaro, L Xie, MD Urbaniak, MAJ Ferguson, ...
PLoS Comput Biol 6 (1), e1000648, 2010
952010
Ensemble docking in drug discovery
RE Amaro, J Baudry, J Chodera, ÷ Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
892018
MM-PBSA captures key role of intercalating water molecules at a protein− protein interface
S Wong, RE Amaro, JA McCammon
Journal of chemical theory and computation 5 (2), 422-429, 2009
892009
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Articles 1–20