Mobley DL - Search Results

1

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks [Article v0.1].

Hahn DF, Bayly CI, Macdonald HEB, Chodera JD, Mey ASJS, Mobley DL, Benito LP, Schindler CEM, Tresadern G, Warren GL. Hahn DF, et al. Among authors: mobley dl. Living J Comput Mol Sci. 2022;4(1):1497. doi: 10.33011/livecoms.4.1.1497. Epub 2022 Aug 30. Living J Comput Mol Sci. 2022. PMID: 36382113 Free PMC article.

2

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.

Mobley DL, Chodera JD, Dill KA. Mobley DL, et al. J Chem Phys. 2006 Aug 28;125(8):084902. doi: 10.1063/1.2221683. J Chem Phys. 2006. PMID: 16965052 Free PMC article.

3

Comparison of charge models for fixed-charge force fields: small-molecule hydration free energies in explicit solvent.

Mobley DL, Dumont E, Chodera JD, Dill KA. Mobley DL, et al. J Phys Chem B. 2007 Mar 8;111(9):2242-54. doi: 10.1021/jp0667442. Epub 2007 Feb 10. J Phys Chem B. 2007. PMID: 17291029

4

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.

5

Accurate and efficient corrections for missing dispersion interactions in molecular simulations.

Shirts MR, Mobley DL, Chodera JD, Pande VS. Shirts MR, et al. Among authors: mobley dl. J Phys Chem B. 2007 Nov 15;111(45):13052-63. doi: 10.1021/jp0735987. Epub 2007 Oct 19. J Phys Chem B. 2007. PMID: 17949030

6

Treating entropy and conformational changes in implicit solvent simulations of small molecules.

Mobley DL, Dill KA, Chodera JD. Mobley DL, et al. J Phys Chem B. 2008 Jan 24;112(3):938-46. doi: 10.1021/jp0764384. Epub 2008 Jan 3. J Phys Chem B. 2008. PMID: 18171044 Free PMC article.

7

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

Nicholls A, Mobley DL, Guthrie JP, Chodera JD, Bayly CI, Cooper MD, Pande VS. Nicholls A, et al. Among authors: mobley dl. J Med Chem. 2008 Feb 28;51(4):769-79. doi: 10.1021/jm070549+. Epub 2008 Jan 24. J Med Chem. 2008. PMID: 18215013

8

The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change.

Mobley DL, Chodera JD, Dill KA. Mobley DL, et al. J Chem Theory Comput. 2007;3(4):1231-1235. doi: 10.1021/ct700032n. J Chem Theory Comput. 2007. PMID: 18843379 Free PMC article.

9

Predictions of hydration free energies from all-atom molecular dynamics simulations.

Mobley DL, Bayly CI, Cooper MD, Dill KA. Mobley DL, et al. J Phys Chem B. 2009 Apr 9;113(14):4533-7. doi: 10.1021/jp806838b. J Phys Chem B. 2009. PMID: 19271713 Free PMC article.

10

Small molecule hydration free energies in explicit solvent: An extensive test of fixed-charge atomistic simulations.

Mobley DL, Bayly CI, Cooper MD, Shirts MR, Dill KA. Mobley DL, et al. J Chem Theory Comput. 2009 Feb 10;5(2):350-358. doi: 10.1021/ct800409d. J Chem Theory Comput. 2009. PMID: 20150953 Free PMC article.

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