Publications and Patents:*

  1. Chen, Lieyang; Cruz, Anthony; Ramsey, Steven; Dickson, Callum J.; Duca, José S.; Hornak, Viktor; Koes, David R; & Tom Kurtzman."Hidden Bias in the DUD-E Dataset Leads to Misleading Performance of Deep Learning in Structure-Based Virtual Screening." ChemRxiv. (Preprint on March 24, 2019) PDF
  2. 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 March 5, 2019) PDF
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. Kamran Haider, Lauren Wickstrom, Steven Ramsey, Michael K. Gilson, & Tom Kurtzman. "Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces" The Journal of Phisical Chemistry Part B (2016) PDF
  12. Satishkumar Gadhiya, Sudharshan Madapa, Tom Kurtzman, Ian L. Alberts, Steven Ramsey, Nagavara-Kishore Pillarsetty, Teja Kalidindi, & Wayne W. Harding. "Tetrahydroprotoberberine alkaloids with dopamine and delta receptor affinity" Bioorganic & Medicinal Chemistry (2016) PDF
  13. Crystal N. Nguyen, Tom Kurtzman & Michael K. Gilson. "Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets" Journal of Chemical Theory and Computation (2015) PDF
  14. Camilo Velez-Vega, Daniel J.J. McKay, Tom Kurtzman, Vibhas Aravamuthan, Robert Pearlstein & Jose Duca. "Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations" Journal of Chemical Theory and Computation (2015) PDF
  15. Wickstrom, Lauren, Nanjie Deng, Peng He, Ahmet Mentes, Crystal Nguyen, Michael K. Gilson, Tom Kurtzman, Emilio Gallicchio, & Ronald M. Levy. "Parameterization of an Effective Potential for Protein-Ligand Binding from Host-Guest Affinity Data." Journal of Molecular Recognition (2015). PDF
  16. Nguyen, Crystal N., Anthony Cruz, Michael K. Gilson, & Tom Kurtzman. "Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa." Journal of Chemical Theory and Computation 10 (2014) PDF
  17. Armaiz-Pena, G. N., Allen, J. K., Cruz, A., Stone, R. L., Nick, A. M., Lin, Y. G., Han, L. Y., Mangala, L. S., Villares, G. J., Vivas-Mejia, P., Rodriguez-Aguayo, C., Nagaraja, A. S., Gharpure, K. M., Wu, Z., English, R. D., Soman, K. V., Shazhad, M. M. K., Zigler, M., Deavers, M. T., Zien, A., Soldatos, T. G., Jackson, D. B., Wiktorowicz, J. E., Torres-Lugo, M., Young, T., Geest, K. De, Gallick, G. E., Bar-Eli, M., Lopez-Berestein, G., Cole, S. W., Lopez, G. E., Lutgendorf, S. K., & Sood, A. K. “Src Activation by β-Adrenoreceptors Is a Key Switch for Tumour Metastasis” Nature Communications 4, (2013): 1403. doi:10.1038/ncomms2413. PDF
  18. Nguyen, C., Kurtzman Young, T. & Gilson, M. K. Inhomogeneous Solvation Theory: Hydration Structure and Thermodynamics of the Miniature Receptor Cucubit[7]uril. The Journal of Chemical Physics (2012). PDF
  19. Nguyen, C., Gilson, M. K. & Young, T. Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory. arXiv:1108.4876 (2011). PDF
  20. Young, T., Abel, R., Friesner, R. A. & Berne, B. J. Methods Of Calculating Differences Of Binding Affinities Between Congeneric Pairs Of Ligands By Way Of A Displaced Solvent Functional, U.S. Patent 7756674, U.S. Patent 7970580, U.S. Patent 7970581. (2011). 7756674, 7970580, 7970581
  21. Young, T. et al. Dewetting transitions in protein cavities. Proteins: Structure, Function, and Bioinformatics 78, 1856–1869 (2010). PDF
  22. Abel, R., Young, T., Farid, R., Berne, B. J. & Friesner, R. A. The role of the active site solvent in the thermodynamics of factor Xa-ligand binding. J Am Chem Soc 130, 2817–2831 (2008). PDF
  23. Young, T., Abel, R., Kim, B., Berne, B. J. & Friesner, R. A. Motifs for molecular recognition exploiting hydrophobic enclosure in protein–ligand binding. Proceedings of the National Academy of Sciences 104, 808 –813 (2007). PDF
  24. Kim, B., Young, T., Harder, E., Friesner, R. A. & Berne, B. J. Structure and Dynamics of the Solvation of Bovine Pancreatic Trypsin Inhibitor in Explicit Water: A Comparative Study of the Effects of Solvent and Protein Polarizability. J Phys Chem B 109, 16529-16538 (2005). PDF
  25. Young, T. & Andersen, H. C. Tests of an approximate scaling principle for dynamics of classical fluids. J Phys Chem B 109, 2985–2994 (2005). PDF
  26. Young, T. & Andersen, H. C. A scaling principle for the dynamics of density fluctuations in atomic liquids. The Journal of Chemical Physics 118, 3447 (2003). PDF
  27. Pitts, S. J., Young, T. & Andersen, H. C. Facilitated spin models, mode coupling theory, and ergodic–nonergodic transitions. The Journal of Chemical Physics 113, 8671 (2000). PDF
*Tom Kurtzman previously published under the family name Young