Publications

Selected Publications (more)

CADD Methods Development

Simulating water exchange to buried binding sites. I Ben-Shalom, C Lin, T Kurtzman, RC Walker, MK Gilson. J Chem Theo Comput 15:2684, 2019, 10.1021/acs.jctc.8b01284

Facile synthesis of a diverse library of mono-3-substituted beta-cyclodextrin analogues. K Kellett, BM Duggan, MK Gilson. Supramolec Chem 31:251, 2019, 10.1080/10610278.2018.1562191

Evaluating force field performance in thermodynamic calculations of cyclodextrin host–guest binding: Water models, partial charges, and host force field parameters. NM Henriksen, MK GIlson. J Chem Theo Comput 13:4253, 2017, 10.1021/acs.jctc.7b00359.

Attach-pull-release calculations of ligand binding and conformational changes on the first BRD4 bromodomain. G Heinzelman, NM Henriksen, MK Gilson. J Chem Theo Comput 13:3260, 2017, 10.1021/acs.jctc.7b00275.

Evaluation and minimization of uncertainty in ITC binding measurements: heat error, concentration error, saturation, and stoichiometry. SA Kantonen, NM Henriksen, MK Gilson. Biochim Biophys Acta Gen Subj 1861:485, 2017, 10.1016/j.bbagen.2016.09.002.

Grid inhomogeneous solvation theory: hydration structure and thermodynamics of the miniature receptor cucurbit [7] uril. CN Nguyen, T Kurtzman, MK Gilson. J Chem Phys 137:044101, 10.1063/1.4733951.

Blinded Prediction Challenges

Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking. JR Wagner, CP Churas, S Liu, RV Swift, M Chiu, C Shao, VA Feher, SK Burley, MK Gilson, RE Amaro. Structure, 2019, in press (as of 4/25/2019).

D3R Grand Challenge 3: blind prediction of protein–ligand poses and affinity rankings. Z Gaieb, CD Parks, M Chiu, H Yang, C Shao, WP Walters, MH Lambert, N Nevins, SD Bembenek, MK Ameriks, T Mirzadegan, SK Burley, RE Amaro, MK Gilson. J Comput-Aided Drug Design 33:1, 2019, 10.1007/s10822-018-0180-4.

Overview of the SAMPL5 host–guest challenge: Are we doing better? J Yin, NM Henriksen, DR Slochower, MR Shirts, MW Chiu, DL Mobley, MK Gilson. J Comput-Aided Drug Design 31:1, 2017, 10.1007/s10822-016-9974-4.

Binding Database

BindingDB in 2015: a public database for medicinal chemistry, computational chemistry and systems pharmacology. MK Gilson, T Liu, M Baitaluk, G Nicola, L Hwang, J Chong. Nucleic Acids Res 44: D1045, 2015, 10.1093/nar/gkv1072.

BindingDB: a web-accessible database of experimentally determined protein–ligand binding affinities. T Liu, Y Lin, X Wen, RN Jorissen, MK Gilson. Nucleic Acids Res 35:D198, 2006, 10.1093/nar/gkl999.

Molecular motors and motions

Motor-like properties of nonmotor enzymes. DR Slochower, MK Gilson. Biophys J 114:2174, 2018, 10.1016/j.bpj.2018.02.008.

A Thermodynamic Limit on the Role of Self-Propulsion in Enhanced Enzyme Diffusion. Biophys J, 2019, in press (4/25/2019)

Translational Research

Discovering de novo peptide substrates for enzymes using machine learning. L Tallorin, JL Wang, WE Kim, S Sahu, NM Kosa, P Yang, M Thompson, MK Gilson, PI Frazier, MD Burkart, NC Gianneschi. Nature Comm 9:5253, 2018, 10.1038/s41467-018-07717-6.

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. KS Lee, NM Henriksen, CJ Ng, J Yang, W Jia, C Morisseau, A Andaya, MK Gilson, BD Hammock. Arch Bioch Biophys 613:1, 2017, 10.1016/j.abb.2016.10.017.

Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. AP Blum, JK Kammeyer, J Yin, DT Crystal, AM Rush, MK Gilson, NC Gianneschi. JACS, 2014, 10.1021/ja5088216.

Supramolecular assembly promotes the electrocatalytic reduction of carbon dioxide by Re (I) bipyridine catalysts at a lower overpotential. CW Machan, SA Chabolla, J Yin, MK Gilson, FA Tezcan, CP Kubiak JACS 136:14598, 2014, 10.1021/ja5085282.

Patents

US Patent 8,140,268. Computational method for drug discovery and receptor design. Inventor: Michael Jason Potter, Hillary Sue Rodman Gilson, Michael Kenneth Gilson. 2009.

US Patent 6,970,791. Tailored user interfaces for molecular modeling. Michael Jason Potter, Hillary Sue Rodman Gilson, Michael Kenneth Gilson. 2005.