Publications and Patents:*

  1. Lauren Wickstrom, Emilio Galicchio, Lieyang Chen, Tom Kurtzman, Nanjie Deng. "Developing End-Point Methods for Absoulte Binding Free Energy Calculation Using the Boltzmann-Quasiharmonic model." Physical Chemistry Chemical Physics (Published on February 21, 2022) PDF
  2. Solmaz Azimi, Joe Z. Wu, Sheenam Khuttan, Tom Kurtzman, Nanjie Deng, Emilio Gallicchio. "Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host‑guest blinded challenge." Journal of Computer-Aided Molecular Design (Published on January 21, 2022) PDF
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. Nguyen, C., Gilson, M. K. & Young, T. Structure and Thermodynamics of Molecular Hydration via Grid Inhomogeneous Solvation Theory. arXiv:1108.4876 (2011). PDF
  28. 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
  29. Young, T. et al. Dewetting transitions in protein cavities. Proteins: Structure, Function, and Bioinformatics 78, 1856–1869 (2010). PDF
  30. 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
  31. 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
  32. 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
  33. 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
  34. 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
  35. 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