Mobley DL - Search Results

1

Molecular-dynamics simulation methods for macromolecular crystallography.

Wych DC, Aoto PC, Vu L, Wolff AM, Mobley DL, Fraser JS, Taylor SS, Wall ME. Wych DC, et al. Among authors: mobley dl. Acta Crystallogr D Struct Biol. 2023 Jan 1;79(Pt 1):50-65. doi: 10.1107/S2059798322011871. Epub 2023 Jan 1. Acta Crystallogr D Struct Biol. 2023. PMID: 36601807 Free PMC article.

2

Predicting absolute ligand binding free energies to a simple model site.

Mobley DL, Graves AP, Chodera JD, McReynolds AC, Shoichet BK, Dill KA. Mobley DL, et al. J Mol Biol. 2007 Aug 24;371(4):1118-34. doi: 10.1016/j.jmb.2007.06.002. Epub 2007 Jun 8. J Mol Biol. 2007. PMID: 17599350 Free PMC article.

3

Blind prediction of charged ligand binding affinities in a model binding site.

Rocklin GJ, Boyce SE, Fischer M, Fish I, Mobley DL, Shoichet BK, Dill KA. Rocklin GJ, et al. Among authors: mobley dl. J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26. J Mol Biol. 2013. PMID: 23896298 Free PMC article.

4

Overview of the SAMPL5 host-guest challenge: Are we doing better?

Yin J, Henriksen NM, Slochower DR, Shirts MR, Chiu MW, Mobley DL, Gilson MK. Yin J, et al. Among authors: mobley dl. J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. J Comput Aided Mol Des. 2017. PMID: 27658802 Free PMC article. Review.

5

Lessons learned from comparing molecular dynamics engines on the SAMPL5 dataset.

Shirts MR, Klein C, Swails JM, Yin J, Gilson MK, Mobley DL, Case DA, Zhong ED. Shirts MR, et al. Among authors: mobley dl. J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. J Comput Aided Mol Des. 2017. PMID: 27787702 Free PMC article.

6

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL. Wall ME, et al. Among authors: mobley dl. J Am Chem Soc. 2019 Mar 20;141(11):4711-4720. doi: 10.1021/jacs.8b13613. Epub 2019 Mar 11. J Am Chem Soc. 2019. PMID: 30834751 Free PMC article.

7

Liquid-like and rigid-body motions in molecular-dynamics simulations of a crystalline protein.

Wych DC, Fraser JS, Mobley DL, Wall ME. Wych DC, et al. Among authors: mobley dl. Struct Dyn. 2019 Dec 18;6(6):064704. doi: 10.1063/1.5132692. eCollection 2019 Nov. Struct Dyn. 2019. PMID: 31867408 Free PMC article.

8

Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics.

Sasmal S, Gill SC, Lim NM, Mobley DL. Sasmal S, et al. Among authors: mobley dl. J Chem Theory Comput. 2020 Mar 10;16(3):1854-1865. doi: 10.1021/acs.jctc.9b01066. Epub 2020 Feb 24. J Chem Theory Comput. 2020. PMID: 32058713 Free PMC article.

9

Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.

Lim NM, Osato M, Warren GL, Mobley DL. Lim NM, et al. Among authors: mobley dl. J Chem Theory Comput. 2020 Apr 14;16(4):2778-2794. doi: 10.1021/acs.jctc.9b01096. Epub 2020 Mar 27. J Chem Theory Comput. 2020. PMID: 32167763 Free PMC article.

10

Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques.

Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL. Ge Y, et al. Among authors: mobley dl. J Chem Theory Comput. 2022 Mar 8;18(3):1359-1381. doi: 10.1021/acs.jctc.1c00590. Epub 2022 Feb 11. J Chem Theory Comput. 2022. PMID: 35148093 Free PMC article.

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