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Recent Publications

Donyapour N, Roussey NM, Dickson A. “REVO: Resampling of ensembles by variation optimization.” J Chem Phys. (2019) Jun 28;150(24):244112. doi: 10.1063/1.5100521

Liu Y, Hickey DP, Minteer SD, Dickson A, Calabrese Barton S. “Markov-State Transition Path Analysis of Electrostatic Channeling.” J Phys Chem C Nanomater Interfaces. (2019) Jun 20;123(24):15284-15292. doi: 10.1021/acs.jpcc.9b02844

Bai N, Roder H, Dickson A, Karanicolas J. “Isothermal Analysis of ThermoFluor Data can readily provide Quantitative Binding Affinities.” Sci Rep. (2019) Feb 25;9(1):2650. doi: 10.1038/s41598-018-37072-x

Kirberger SE, Ycas PD, Johnson JA, Chen C, Ciccone MF, Woo RWL, Urick AK, Zahid H, Shi K, Aihara H, McAllister SD, Kashani-Sabet M, Shi J, Dickson A, Dos Santos CO, Pomerantz WCK. “Selectivity, ligand deconstruction, and cellular activity analysis of a BPTF bromodomain inhibitor.” Org Biomol Chem. (2019) Feb 1. doi: 10.1039/c8ob02599a

Dickson A. “Mapping the Ligand Binding Landscape.” Biophys J. (2018) Sep 29. doi: 10.1016/j.bpj.2018.09.021

Dixon T, Lotz SD, Dickson A. “Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.” J Comput Aided Mol Des. (2018) Aug 23. doi: 10.1007/s10822-018-0149-3

Zeng X, Uyar A, Sui D, Donyapour N, Wu D, Dickson A, Hu J. “Structural Insights into Lethal Contractural Syndrome Type 3 (LCCS3) Caused by a Missense Mutation of PIP5Kγ.” Biochem J. (2018) Jun 29. doi: 10.1042/BCJ20180326

Wood RJ, Ormsby AR, Radwan M, Cox D, Sharma A, Vöpel T, Ebbinghaus S, Oliveberg M, Reid GE, Dickson A, Hatters DM. “A biosensor-based framework to measure latent proteostasis capacity.” Nat Commun. (2018) Jan 18;9(1):287. doi: 10.1038/s41467-017-02562-5

Lotz SD, Dickson A. “Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions.” J Am Chem Soc. (2018) Jan 5;. doi: 10.1021/jacs.7b08572

Uyar A, Karamyan VT, Dickson A. “Long-Range Changes in Neurolysin Dynamics Upon Inhibitor Binding.” J Chem Theory Comput. (2017) Dec 8;. doi: 10.1021/acs.jctc.7b00944

Dickson A, Tiwary P, Vashisth H. “Kinetics of Ligand Binding Through Advanced Computational Approaches: A Review.” Curr Top Med Chem. (2017) Apr 14. doi: 10.2174/1568026617666170414142908

Dickson A, Lotz SD. “Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.” Biophys J. (2017) Feb 28;112(4):620-629. doi: 10.1016/j.bpj.2017.01.006

Dickson A, Bailey CT, Karanicolas J. “Optimal allosteric stabilization sites using contact stabilization analysis.” J Comput Chem. (2016) Oct 24. doi: 10.1002/jcc.24517

Dickson A, Lotz SD. “Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.” J Phys Chem B. (2016) Jun 8. doi:10.1021/acs.jpcb.6b04012

Dickson A, Ahlstrom LS, Brooks CL 3rd. "Coupled folding and binding with 2D Window-Exchange Umbrella Sampling." J Comput Chem. (2015) Aug 6. doi: 10.1002/jcc.24004

Laricheva EN, Goh GB, Dickson A, Brooks CL 3rd. "pH-dependent transient conformational states control optical properties in cyan fluorescent protein." J Am Chem Soc. (2015) Mar 4;137(8):2892-900. doi: 10.1021/ja509233r

Ahlstrom LS, Law SM, Dickson A, Brooks CL 3rd. "Multiscale modeling of a conditionally disordered pH-sensing chaperone." J Mol Biol. (2015) Apr 24;427(8):1670-80. doi: 10.1016/j.jmb.2015.01.002

Dickson A, Mustoe AM, Salmon L, Brooks CL 3rd. "Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore." Nucleic Acids Res. (2014) Oct 29;42(19):12126-37. doi: 10.1093/nar/gku799

Dickson A, Brooks CL 3rd. "WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm." J Phys Chem B. (2014) Apr 3;118(13):3532-42. doi: 10.1021/jp411479c

Dickson A, Brooks CL 3rd. "Quantifying chaperone-mediated transitions in the proteostasis network of E. coli." PLoS Comput Biol. (2013);9(11):e1003324. doi: 10.1371/journal.pcbi.1003324

Ahlstrom LS, Dickson A, Brooks CL 3rd. "Binding and folding of the small bacterial chaperone HdeA." J Phys Chem B. (2013) Oct 24;117(42):13219-25. doi: 10.1021/jp403264s

Dickson A, Brooks CL 3rd. "Native states of fast-folding proteins are kinetic traps." J Am Chem Soc. (2013) Mar 27;135(12):4729-34. doi: 10.1021/ja311077u

Dickson A, Brooks CL 3rd. "Quantifying hub-like behavior in protein folding networks." J Chem Theory Comput. (2012);8(9):3044-3052

Dickson A, Tabei SM, Dinner AR. "Entrainment of a driven oscillator as a dynamical phase transition." Phys Rev E Stat Nonlin Soft Matter Phys. (2011) Dec;84(6 Pt 1):061134