Thomas Kurtzman

Research in the Kurtzman lab focuses on the development of computational methods that aid in the discovery and rational design of new drugs. Our approach applies a combination of statistical mechanical theory and computer simulations to better understand the physical principles governing the molecular recognition between proteins and small molecule drug candidates. His research contributions provide a framework to account for and quantify the role that water plays in molecular recognition.

Selected Publications

• Lieyang Chen, Anthony Cruz, Daniel R. Roe, Andrew C. Simmonett, Lauren Wickstrom, Nanjie Deng, Tom Kurtzman*. "Thermodynamic decomposition of solvation free energies with particle mesh Ewald and long-range Lennard-Jones interactions in Grid Inhomogeneous Solvation Theory." Journal of Chemical Theory and Computation (Published on April 8, 2021) PDF
• Brian Olson, Anthony Cruz, Lieyang Chen, Mossa Ghattas, Yeonji Ji, Kunhui Huang, Steven Ayoub Jr, Tyler Luchko, Daniel J. McKay, Tom Kurtzman*. "An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets." Journal of Computer-Aided Molecular Design (Published on August 29, 2020) PDF
• D.A. Case, K. Belfon, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, G. Giambasu, M.K. Gilson, H. Gohlke, A.W. Goetz, R. Harris, S. Izadi, S.A. Izmailov, K. Kasavajhala, A. Kovalenko, R. Krasny, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, V. Man, K.M. Merz, Y. Miao, O. Mikhailovskii, G. Monard, H. Nguyen, A. Onufriev, F.Pan, S. Pantano, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C. Simmerling, N.R.Skrynnikov, J. Smith, J. Swails, R.C. Walker, J. Wang, L. Wilson, R.M. Wolf, X. Wu, Y. Xiong, Y. Xue, D.M. York and P.A. Kollman (2020), AMBER 2020, University of California, San Francisco. (Published on April 15, 2020) PDF
• Pal RK, Gadhiya S, Ramsey S, Cordone P, Wickstrom L, Harding WW, Tom Kurtzman, Emilio Gallicchio. "Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes." PLOS ONE (Published on September 30, 2019) PDF
• Peng He, Sheila Sarkar, Emilio Gallicchio, Tom Kurtzman and Lauren Wickstrom*. "Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin". The Journal of Physical Chemistry B (Published on September 13, 2019) PDF
• Lieyang Chen, Anthony Cruz, Steven Ramsey,Callum J. Dickson, José S. Duca, Viktor Hornak, David R. Koes, & Tom Kurtzman*."Hidden Bias in the DUD-E Dataset Leads to Misleading Performance of Deep Learning in Structure-Based Virtual Screening." PLOS ONE (Published on August 20, 2019) PDF
• Crystal Nguyen, Takeshi Yamazaki, Andriy Kovalenko, David A. Case, Michael K. Gilson*, Tom Kurtzman*, Tyler Luchko*. "A Molecular Reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site." PLOS ONE (Published on July 10, 2019) PDF
• Ido Y. Ben-Shalom, Charles Lin, Tom Kurtzman, Ross C. Walker, & Michael K.Gilson "Simulating Water Exchange to Buried Binding Sites." J. Chem. Theory Comput. (published on March 5, 2019) PDF
• Satishkumar Gadhiya, Pierpaolo Cordone, Rajat K. Pal, Emilio Gallicchio, Lauren Wickstrom, Tom Kurtzman, Steven Ramsey, & Wayne W. Harding. "New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif." ACS Medicinal Chemistry Letters (Published September 10, 2018) PDF
• Sang Won Jung, Minsup Kim, Steven Ramsey, Tom Kurtzman, & Art E. Cho. "Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water." Scientific Report (Published July 10, 2018) PDF
• D.A. Case, I.Y. Ben-Shalom, S.R. Brozell, D.S. Cerutti, T.E. Cheatham, III, V.W.D. Cruzeiro, T.A. Darden, R.E. Duke, D. Ghoreishi, M.K. Gilson, H. Gohlke, A.W. Goetz, D. Greene, R Harris, N. Homeyer, Y. Huang, S. Izadi, A. Kovalenko, T. Kurtzman, T.S. Lee, S. LeGrand, P. Li, C. Lin, J. Liu, T. Luchko, R. Luo, D.J. Mermelstein, K.M. Merz, Y. Miao, G. Monard, C. Nguyen, H. Nguyen, I. Omelyan, A. Onufriev, F. Pan, R. Qi, D.R. Roe, A. Roitberg, C. Sagui, S. Schott-Verdugo, J. Shen, C.L. Simmerling, J. Smith, R. SalomonFerrer, J. Swails, R.C. Walker, J. Wang, H. Wei, R.M. Wolf, X. Wu, L. Xiao, D.M. York and P.A. Kollman (2018), AMBER 2018, University of California, San Francisco. (Published April 17, 2018) PDF
• Kamran Haider, Anthony Cruz, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Solvation Structure and Thermodynamic Mapping (SSTMap): An open-source, flexible package for the analysis of water in molecular dynamics trajectories." Journal of Chemical Theory and Computation (Published November 21, 2017) PDF
• Trent E. Balius, Marcus Fischer, Reed M. Stein, Thomas B. Adler, Crystal N. Nguyen, Anthony Cruz, Michael K. Gilson, Tom Kurtzman, & Brian K. Shoichet. "Testing Inhomogeneous Solvation Theory in Structure-Based Ligand Discovery" Proceedings of the National Academy of Sciences (Published July 31, 2017) PDF
• Pal, R.K., Haider, K., Kaur, Divya, Flynn, W., Xia, J., Levy, R.M., Taran, T., Wickstrom, L., Kurtzman, T., & Gallicchio, E. "A Combined Treatment of Hydration and Dynamical Effects for the Modeling of Host-Guest Binding Thermodynamics: The SAMPL5 Blinded Challenge" Journal of Computer-Aided Molecular Design (Published January 15th, 2017) PDF
• Madapa, S., Gadhiya, S., Kurtzman T., Alberts I.L., Ramsey S., Reith, M.E., & Harding, W.W. "Synthesis and Evaluation of C9 Alkoxy Analogues of (-)-Stepholidine as Dopamine Receptor Ligands" European Journal of Medicinal Chemistry (Published January 5th, 2017) PDF
• Steven Ramsey, Crystal Nguyen, Romelia Salomon-Ferrer, Ross C. Walker, Michael K. Gilson, & Tom Kurtzman. "Solvation Thermodynamic Mapping of Molecular Surfaces in AmberTools: GIST" Journal of Computational Chemistry (Published August 5th, 2016) PDF