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Tom Kurtzman - Publications

Affiliations: 
Lehman College 
Area:
Computational/Theoretical Chemistry
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Wickstrom L, Gallicchio E, Chen L, Kurtzman T, Deng N. Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model. Physical Chemistry Chemical Physics : Pccp. PMID 35212338 DOI: 10.1039/d1cp05075c  0.667
2022 Azimi S, Wu JZ, Khuttan S, Kurtzman T, Deng N, Gallicchio E. Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge. Journal of Computer-Aided Molecular Design. 36: 63-76. PMID 35059940 DOI: 10.1007/s10822-021-00437-y  0.658
2020 Olson B, Cruz A, Chen L, Ghattas M, Ji Y, Huang K, McKay DJ, Kurtzman T. An Online Repository of Solvation Thermodynamic and Structural Maps of SARS-CoV-2 Targets. Chemrxiv : the Preprint Server For Chemistry. PMID 32511289 DOI: 10.1007/S10822-020-00341-X  0.352
2020 Ben-Shalom IY, Lin C, Kurtzman T, Walker R, Gilson MK. Equilibration of Buried Water Molecules to Enhance Protein-Ligand Binding Free Energy Calculations Biophysical Journal. 118: 144a. DOI: 10.1016/J.Bpj.2019.11.908  0.51
2019 Pal RK, Gadhiya S, Ramsey S, Cordone P, Wickstrom L, Harding WW, Kurtzman T, Gallicchio E. Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes. Plos One. 14: e0222902. PMID 31568493 DOI: 10.1371/Journal.Pone.0222902  0.77
2019 He P, Sarkar S, Gallicchio E, Kurtzman T, Wickstrom L. The Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin. The Journal of Physical Chemistry. B. PMID 31509409 DOI: 10.1021/Acs.Jpcb.9B07028  0.631
2019 Chen L, Cruz A, Ramsey S, Dickson CJ, Duca JS, Hornak V, Koes DR, Kurtzman T. Hidden bias in the DUD-E dataset leads to misleading performance of deep learning in structure-based virtual screening. Plos One. 14: e0220113. PMID 31430292 DOI: 10.1371/Journal.Pone.0220113  0.72
2019 Nguyen C, Yamazaki T, Kovalenko A, Case DA, Gilson MK, Kurtzman T, Luchko T. A molecular reconstruction approach to site-based 3D-RISM and comparison to GIST hydration thermodynamic maps in an enzyme active site. Plos One. 14: e0219473. PMID 31291328 DOI: 10.1371/Journal.Pone.0219473  0.445
2019 Ben-Shalom IY, Lin C, Kurtzman T, Walker RC, Gilson MK. Simulating Water Exchange to Buried Binding Sites. Journal of Chemical Theory and Computation. PMID 30835999 DOI: 10.1021/Acs.Jctc.8B01284  0.443
2018 Gadhiya S, Cordone P, Pal RK, Gallicchio E, Wickstrom L, Kurtzman T, Ramsey S, Harding WW. New Dopamine D3-Selective Receptor Ligands Containing a 6-Methoxy-1,2,3,4-tetrahydroisoquinolin-7-ol Motif. Acs Medicinal Chemistry Letters. 9: 990-995. PMID 30344905 DOI: 10.1021/Acsmedchemlett.8B00229  0.753
2018 Jung SW, Kim M, Ramsey S, Kurtzman T, Cho AE. Water Pharmacophore: Designing Ligands using Molecular Dynamics Simulations with Water. Scientific Reports. 8: 10400. PMID 29991756 DOI: 10.1038/S41598-018-28546-Z  0.744
2017 Haider K, Cruz A, Ramsey S, Gilson MK, Kurtzman T. 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. PMID 29161510 DOI: 10.1021/Acs.Jctc.7B00592  0.741
2017 Balius TE, Fischer M, Stein RM, Adler TB, Nguyen CN, Cruz A, Gilson MK, Kurtzman T, Shoichet BK. Testing inhomogeneous solvation theory in structure-based ligand discovery. Proceedings of the National Academy of Sciences of the United States of America. PMID 28760952 DOI: 10.1073/Pnas.1703287114  0.502
2016 Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, Taran T, Wickstrom L, Kurtzman T, Gallicchio E. Erratum to: 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. PMID 27815770 DOI: 10.1007/s10822-016-9987-z  0.615
2016 Pal RK, Haider K, Kaur D, Flynn W, Xia J, Levy RM, 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. PMID 27696239 DOI: 10.1007/S10822-016-9956-6  0.699
2016 Madapa S, Gadhiya S, Kurtzman T, Alberts IL, Ramsey S, Reith M, Harding WW. Synthesis and evaluation of C9 alkoxy analogues of (-)-stepholidine as dopamine receptor ligands. European Journal of Medicinal Chemistry. 125: 255-268. PMID 27688181 DOI: 10.1016/J.Ejmech.2016.09.036  0.724
2016 Ramsey S, Nguyen C, Salomon-Ferrer R, Walker RC, Gilson MK, Kurtzman T. Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST. Journal of Computational Chemistry. 37: 2029-37. PMID 27317094 DOI: 10.1002/Jcc.24417  0.721
2016 Haider K, Wickstrom L, Ramsey S, Gilson MK, Kurtzman T. Enthalpic Breakdown of Water Structure on Protein Active-Site Surfaces. The Journal of Physical Chemistry. B. 120: 8743-56. PMID 27169482 DOI: 10.1021/Acs.Jpcb.6B01094  0.73
2016 Gadhiya S, Madapa S, Kurtzman T, Alberts IL, Ramsey S, Pillarsetty NK, Kalidindi T, Harding WW. Tetrahydroprotoberberine alkaloids with dopamine and σ receptor affinity. Bioorganic & Medicinal Chemistry. PMID 27032890 DOI: 10.1016/J.Bmc.2016.03.037  0.727
2016 Nguyen CN, Kurtzman T, Gilson MK. Spatial Decomposition of Translational Water-Water Correlation Entropy in Binding Pockets. Journal of Chemical Theory and Computation. 12: 414-29. PMID 26636620 DOI: 10.1021/Acs.Jctc.5B00939  0.432
2016 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data. Journal of Molecular Recognition : Jmr. 29: 10-21. PMID 26256816 DOI: 10.1002/Jmr.2489  0.687
2015 Velez-Vega C, McKay DJ, Kurtzman T, Aravamuthan V, Pearlstein RA, Duca JS. Estimation of Solvation Entropy and Enthalpy via Analysis of Water Oxygen-Hydrogen Correlations. Journal of Chemical Theory and Computation. 11: 5090-102. PMID 26574307 DOI: 10.1021/Acs.Jctc.5B00439  0.405
2015 Wickstrom L, Deng N, He P, Mentes A, Nguyen C, Gilson MK, Kurtzman T, Gallicchio E, Levy RM. Parameterization of an effective potential for protein-ligand binding from host-guest affinity data Journal of Molecular Recognition. DOI: 10.1002/jmr.2489  0.642
2014 Nguyen CN, Cruz A, Gilson MK, Kurtzman T. Thermodynamics of Water in an Enzyme Active Site: Grid-Based Hydration Analysis of Coagulation Factor Xa. Journal of Chemical Theory and Computation. 10: 2769-2780. PMID 25018673 DOI: 10.1021/Ct401110X  0.46
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