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Lauren Wickstrom, Ph.D. - Publications

Affiliations: 
2009 Stony Brook University, Stony Brook, NY, United States 
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23 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  0.361
2021 Chen L, Cruz A, Roe DR, Simmonett AC, Wickstrom L, Deng N, Kurtzman T. 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. PMID 33830762 DOI: 10.1021/acs.jctc.0c01185  0.696
2020 Tse C, Wickstrom L, Kvaratskhelia M, Gallicchio E, Levy R, Deng N. Exploring the Free-Energy Landscape and Thermodynamics of Protein-Protein Association. Biophysical Journal. PMID 32877664 DOI: 10.1016/J.Bpj.2020.08.005  0.419
2020 Cruz J, Wickstrom L, Yang D, Gallicchio E, Deng N. Combining Alchemical Transformation with Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites. Journal of Chemical Theory and Computation. PMID 32101691 DOI: 10.1021/Acs.Jctc.9B01119  0.374
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  0.422
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  0.451
2019 Deng N, Xia J, Wickstrom L, Lin C, Wang K, He P, Yin Y, Yang D. Ligand Selectivity in the Recognition of Protoberberine Alkaloids by Hybrid-2 Human Telomeric G-Quadruplex: Binding Free Energy Calculation, Fluorescence Binding, and NMR Experiments. Molecules (Basel, Switzerland). 24. PMID 31010072 DOI: 10.3390/Molecules24081574  0.393
2017 Deng N, Wickstrom L, Cieplak P, Lin C, Yang D. Resolving the Ligand Binding Specificity in C-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment. The Journal of Physical Chemistry. B. PMID 29086571 DOI: 10.1021/Acs.Jpcb.7B09406  0.326
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  0.45
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  0.337
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  0.428
2015 Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C. ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB. Journal of Chemical Theory and Computation. 11: 3696-713. PMID 26574453 DOI: 10.1021/Acs.Jctc.5B00255  0.705
2015 Deng N, Forli S, He P, Perryman A, Wickstrom L, Vijayan RS, Tiefenbrunn T, Stout D, Gallicchio E, Olson AJ, Levy RM. Distinguishing binders from false positives by free energy calculations: fragment screening against the flap site of HIV protease. The Journal of Physical Chemistry. B. 119: 976-88. PMID 25189630 DOI: 10.1021/Jp506376Z  0.415
2014 Gallicchio E, Deng N, He P, Wickstrom L, Perryman AL, Santiago DN, Forli S, Olson AJ, Levy RM. Virtual screening of integrase inhibitors by large scale binding free energy calculations: the SAMPL4 challenge. Journal of Computer-Aided Molecular Design. 28: 475-90. PMID 24504704 DOI: 10.1007/S10822-014-9711-9  0.455
2013 Wickstrom L, He P, Gallicchio E, Levy RM. Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process. Journal of Chemical Theory and Computation. 9: 3136-3150. PMID 25147485 DOI: 10.1021/Ct400003R  0.466
2012 Wickstrom L, Gallicchio E, Levy RM. The linear interaction energy method for the prediction of protein stability changes upon mutation. Proteins. 80: 111-25. PMID 22038697 DOI: 10.1002/Prot.23168  0.347
2011 Shang Y, Nguyen H, Wickstrom L, Okur A, Simmerling C. Improving the description of salt bridge strength and geometry in a Generalized Born model. Journal of Molecular Graphics & Modelling. 29: 676-84. PMID 21168352 DOI: 10.1016/J.Jmgm.2010.11.013  0.747
2009 Wickstrom L, Okur A, Simmerling C. Evaluating the performance of the ff99SB force field based on NMR scalar coupling data. Biophysical Journal. 97: 853-6. PMID 19651043 DOI: 10.1016/J.Bpj.2009.04.063  0.718
2008 Okur A, Wickstrom L, Simmerling C. Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models. Journal of Chemical Theory and Computation. 4: 488-98. PMID 26620789 DOI: 10.1021/Ct7002308  0.759
2007 Wickstrom L, Bi Y, Hornak V, Raleigh DP, Simmerling C. Reconciling the solution and X-ray structures of the villin headpiece helical subdomain: molecular dynamics simulations and double mutant cycles reveal a stabilizing cation-pi interaction. Biochemistry. 46: 3624-34. PMID 17338549 DOI: 10.1021/Bi061785+  0.668
2007 Roe DR, Okur A, Wickstrom L, Hornak V, Simmerling C. Secondary structure bias in generalized Born solvent models: comparison of conformational ensembles and free energy of solvent polarization from explicit and implicit solvation. The Journal of Physical Chemistry. B. 111: 1846-57. PMID 17256983 DOI: 10.1021/Jp066831U  0.737
2006 Okur A, Wickstrom L, Layten M, Geney R, Song K, Hornak V, Simmerling C. Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model. Journal of Chemical Theory and Computation. 2: 420-33. PMID 26626529 DOI: 10.1021/Ct050196Z  0.759
2006 Wickstrom L, Okur A, Song K, Hornak V, Raleigh DP, Simmerling CL. The unfolded state of the villin headpiece helical subdomain: computational studies of the role of locally stabilized structure. Journal of Molecular Biology. 360: 1094-107. PMID 16797585 DOI: 10.1016/J.Jmb.2006.04.070  0.719
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