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Akademický článek

How Robust Is the Ligand Binding Transition State?

Autor: Bose S; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States., Lotz SD; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States., Deb I; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States., Shuck M; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States., Lee KSS; Department of Pharmacology and Toxicology, Michigan State University, East Lansing, Michigan 48824, United States.; Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, United States.; Institute of Integrative Toxicology, Michigan State University, East Lansing, Michigan 48824, United States., Dickson A; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, Michigan 48824, United States.

Publikováno v: Journal of the American Chemical Society [J Am Chem Soc] 2023 Nov 22; Vol. 145 (46), pp. 25318-25331. Date of Electronic Publication: 2023 Nov 09.

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Akademický článek

Creating Maps of the Ligand Binding Landscape for Kinetics-Based Drug Discovery.

Autor: Dixon T; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA., Lotz SD; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.; Roivant Sciences, New York, NY, USA., Dickson A; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA. alexrd@msu.edu.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA. alexrd@msu.edu.

Publikováno v: Methods in molecular biology (Clifton, N.J.) [Methods Mol Biol] 2022; Vol. 2385, pp. 325-334.

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Akademický článek

Wepy: A Flexible Software Framework for Simulating Rare Events with Weighted Ensemble Resampling.

Autor: Lotz SD; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing 48824, Michigan, United States., Dickson A; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing 48824, Michigan, United States.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing 48824, Michigan, United States.

Publikováno v: ACS omega [ACS Omega] 2020 Dec 02; Vol. 5 (49), pp. 31608-31623. Date of Electronic Publication: 2020 Dec 02 (Print Publication: 2020).

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Akademický článek

Predicting ligand binding affinity using on- and off-rates for the SAMPL6 SAMPLing challenge.

Autor: Dixon T; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA., Lotz SD; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA., Dickson A; Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA. alexrd@msu.edu.; Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, 48824, USA. alexrd@msu.edu.

Publikováno v: Journal of computer-aided molecular design [J Comput Aided Mol Des] 2018 Oct; Vol. 32 (10), pp. 1001-1012. Date of Electronic Publication: 2018 Aug 23.

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Akademický článek

Unbiased Molecular Dynamics of 11 min Timescale Drug Unbinding Reveals Transition State Stabilizing Interactions.

Autor: Lotz SD; Michigan State University , East Lansing, Michigan 48823, United States., Dickson A; Michigan State University , East Lansing, Michigan 48823, United States.

Publikováno v: Journal of the American Chemical Society [J Am Chem Soc] 2018 Jan 17; Vol. 140 (2), pp. 618-628. Date of Electronic Publication: 2018 Jan 05.

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Akademický článek

Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.

Autor: Dickson A; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan; Department of Computational Mathematics, Science, and Engineering, Michigan State University, East Lansing, Michigan. Electronic address: alexrd@msu.edu., Lotz SD; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan.

Publikováno v: Biophysical journal [Biophys J] 2017 Feb 28; Vol. 112 (4), pp. 620-629.

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Akademický článek

Ligand Release Pathways Obtained with WExplore: Residence Times and Mechanisms.

Autor: Dickson A; Department of Biochemistry & Molecular Biology and ‡Department of Computational Mathematics, Science and Engineering, Michigan State University , East Lansing, Michigan 48824, United States., Lotz SD; Department of Biochemistry & Molecular Biology and ‡Department of Computational Mathematics, Science and Engineering, Michigan State University , East Lansing, Michigan 48824, United States.

Publikováno v: The journal of physical chemistry. B [J Phys Chem B] 2016 Jun 23; Vol. 120 (24), pp. 5377-85. Date of Electronic Publication: 2016 Jun 08.

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