|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|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
|Emerging methods for ensemble-based virtual screening|
RE Amaro, WW Li
Current topics in medicinal chemistry 10 (1), 3-13, 2010
|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
|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
|Computational approaches to mapping allosteric pathways|
VA Feher, JD Durrant, AT Van Wart, RE Amaro
Current opinion in structural biology 25, 98-103, 2014
|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
|Ensemble docking in drug discovery|
RE Amaro, J Baudry, J Chodera, ÷ Demir, JA McCammon, Y Miao, ...
Biophysical journal 114 (10), 2271-2278, 2018
|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