A suite of tutorials for the WESTPA rare-events sampling software [Article v1. 0] AT Bogetti, B Mostofian, A Dickson, AJ Pratt, AS Saglam, PO Harrison, ... Living journal of computational molecular science 1 (2), 2019 | 716 | 2019 |
Isothermal analysis of ThermoFluor data can readily provide quantitative binding affinities N Bai, H Roder, A Dickson, J Karanicolas Scientific reports 9 (1), 2650, 2019 | 128 | 2019 |
Unbiased molecular dynamics of 11 min timescale drug unbinding reveals transition state stabilizing interactions SD Lotz, A Dickson Journal of the American Chemical Society 140 (2), 618-628, 2018 | 123 | 2018 |
The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations A Rizzi, T Jensen, DR Slochower, M Aldeghi, V Gapsys, D Ntekoumes, ... Journal of computer-aided molecular design 34 (5), 601-633, 2020 | 111 | 2020 |
WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm A Dickson, CL Brooks III Journal of Physical Chemistry B, 2014 | 111 | 2014 |
Enhanced sampling of nonequilibrium steady states A Dickson, AR Dinner Annual review of physical chemistry 61 (1), 441-459, 2010 | 97 | 2010 |
Nonequilibrium umbrella sampling in spaces of many order parameters A Dickson, A Warmflash, AR Dinner The Journal of chemical physics 130 (7), 2009 | 90 | 2009 |
Multiple ligand unbinding pathways and ligand-induced destabilization revealed by WExplore A Dickson, SD Lotz Biophysical journal 112 (4), 620-629, 2017 | 87 | 2017 |
Separating forward and backward pathways in nonequilibrium umbrella sampling A Dickson, A Warmflash, AR Dinner The Journal of chemical physics 131 (15), 2009 | 80 | 2009 |
Ligand release pathways obtained with WExplore: residence times and mechanisms A Dickson, SD Lotz The Journal of Physical Chemistry B 120 (24), 5377-5385, 2016 | 58 | 2016 |
REVO: Resampling of ensembles by variation optimization N Donyapour, NM Roussey, A Dickson The Journal of chemical physics 150 (24), 2019 | 57 | 2019 |
Native states of fast-folding proteins are kinetic traps A Dickson, CL Brooks III Journal of the American Chemical Society 135 (12), 4729-4734, 2013 | 54 | 2013 |
Kinetics of ligand binding through advanced computational approaches: a review A Dickson, P Tiwary, H Vashisth Current topics in medicinal chemistry 17 (23), 2626-2641, 2017 | 53 | 2017 |
Mapping the Ligand Binding Landscape A Dickson Biophysical Journal 115 (9), 1707-1719, 2018 | 45 | 2018 |
Flow-dependent unfolding and refolding of an RNA by nonequilibrium umbrella sampling A Dickson, M Maienschein-Cline, A Tovo-Dwyer, JR Hammond, ... Journal of Chemical Theory and Computation 7 (9), 2710-2720, 2011 | 44 | 2011 |
A biosensor-based framework to measure latent proteostasis capacity RJ Wood, AR Ormsby, M Radwan, D Cox, A Sharma, T Vöpel, ... Nature communications 9 (1), 287, 2018 | 41 | 2018 |
Predicting ligand binding affinity using on-and off-rates for the SAMPL6 SAMPLing challenge T Dixon, SD Lotz, A Dickson Journal of computer-aided molecular design 32 (10), 1001-1012, 2018 | 39 | 2018 |
On calculating free energy differences using ensembles of transition paths R Hall, T Dixon, A Dickson Frontiers in molecular biosciences 7, 106, 2020 | 38 | 2020 |
Membrane-mediated ligand unbinding of the PK-11195 ligand from TSPO T Dixon, A Uyar, S Ferguson-Miller, A Dickson Biophysical journal 120 (1), 158-167, 2021 | 34 | 2021 |
Multiscale modeling of a conditionally disordered pH-sensing chaperone LS Ahlstrom, SM Law, A Dickson, CL Brooks III Journal of molecular biology 427 (8), 1670-1680, 2015 | 33 | 2015 |