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Items: 1 to 50 of 83

1.

Binding thermodynamics of host-guest systems with SMIRNOFF99Frosst 1.0.5 from the Open Force Field Initiative.

Slochower DR, Henriksen NM, Wang LP, Chodera JD, Mobley DL, Gilson M.

J Chem Theory Comput. 2019 Oct 11. doi: 10.1021/acs.jctc.9b00748. [Epub ahead of print]

PMID:
31603667
2.

Binding Modes and Metabolism of Caffeine.

Jandova Z, Gill SC, Lim NM, Mobley DL, Oostenbrink C.

Chem Res Toxicol. 2019 Jul 15;32(7):1374-1383. doi: 10.1021/acs.chemrestox.9b00030. Epub 2019 Jun 11.

3.

Infinite Dilution Activity Coefficients as Constraints for Force Field Parametrization and Method Development.

Duarte Ramos Matos G, Calabrò G, Mobley DL.

J Chem Theory Comput. 2019 May 14;15(5):3066-3074. doi: 10.1021/acs.jctc.8b01029. Epub 2019 Apr 15.

4.

Biomolecular Solvation Structure Revealed by Molecular Dynamics Simulations.

Wall ME, Calabró G, Bayly CI, Mobley DL, Warren GL.

J Am Chem Soc. 2019 Mar 20;141(11):4711-4720. doi: 10.1021/jacs.8b13613. Epub 2019 Mar 11.

PMID:
30834751
5.

Understanding the role of intermolecular interactions between lissoclimides and the eukaryotic ribosome.

Pellegrino S, Meyer M, Könst ZA, Holm M, Voora VK, Kashinskaya D, Zanette C, Mobley DL, Yusupova G, Vanderwal CD, Blanchard SC, Yusupov M.

Nucleic Acids Res. 2019 Apr 8;47(6):3223-3232. doi: 10.1093/nar/gkz053.

6.

Assessing the Conformational Equilibrium of Carboxylic Acid via Quantum Mechanical and Molecular Dynamics Studies on Acetic Acid.

Lim VT, Bayly CI, Fusti-Molnar L, Mobley DL.

J Chem Inf Model. 2019 May 28;59(5):1957-1964. doi: 10.1021/acs.jcim.8b00835. Epub 2019 Feb 21.

PMID:
30742770
7.

Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.

Burley KH, Gill SC, Lim NM, Mobley DL.

J Chem Theory Comput. 2019 Mar 12;15(3):1848-1862. doi: 10.1021/acs.jctc.8b01018. Epub 2019 Feb 11.

8.

Challenges in the use of atomistic simulations to predict solubilities of drug-like molecules.

Duarte Ramos Matos G, Mobley DL.

Version 2. F1000Res. 2018 May 31 [revised 2019 Jan 1];7:686. doi: 10.12688/f1000research.14960.2. eCollection 2018.

9.

Toward Learned Chemical Perception of Force Field Typing Rules.

Zanette C, Bannan CC, Bayly CI, Fass J, Gilson MK, Shirts MR, Chodera JD, Mobley DL.

J Chem Theory Comput. 2019 Jan 8;15(1):402-423. doi: 10.1021/acs.jctc.8b00821. Epub 2018 Dec 24.

PMID:
30512951
10.

Overview of the SAMPL6 host-guest binding affinity prediction challenge.

Rizzi A, Murkli S, McNeill JN, Yao W, Sullivan M, Gilson MK, Chiu MW, Isaacs L, Gibb BC, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):937-963. doi: 10.1007/s10822-018-0170-6. Epub 2018 Nov 10.

PMID:
30415285
11.

pKa measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments.

Işık M, Levorse D, Rustenburg AS, Ndukwe IE, Wang H, Wang X, Reibarkh M, Martin GE, Makarov AA, Mobley DL, Rhodes T, Chodera JD.

J Comput Aided Mol Des. 2018 Oct;32(10):1117-1138. doi: 10.1007/s10822-018-0168-0. Epub 2018 Nov 7.

PMID:
30406372
12.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.

PMID:
30351006
13.

SAMPL6 challenge results from [Formula: see text] predictions based on a general Gaussian process model.

Bannan CC, Mobley DL, Skillman AG.

J Comput Aided Mol Des. 2018 Oct;32(10):1165-1177. doi: 10.1007/s10822-018-0169-z. Epub 2018 Oct 15.

PMID:
30324305
14.

Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages.

Loeffler HH, Bosisio S, Duarte Ramos Matos G, Suh D, Roux B, Mobley DL, Michel J.

J Chem Theory Comput. 2018 Nov 13;14(11):5567-5582. doi: 10.1021/acs.jctc.8b00544. Epub 2018 Oct 22.

PMID:
30289712
15.

Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges.

Riquelme M, Lara A, Mobley DL, Verstraelen T, Matamala AR, Vöhringer-Martinez E.

J Chem Inf Model. 2018 Sep 24;58(9):1779-1797. doi: 10.1021/acs.jcim.8b00180. Epub 2018 Aug 31.

16.

Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain.

Kyrychenko A, Lim NM, Vasquez-Montes V, Rodnin MV, Freites JA, Nguyen LP, Tobias DJ, Mobley DL, Ladokhin AS.

J Membr Biol. 2018 Jun;251(3):379-391. doi: 10.1007/s00232-018-0030-2. Epub 2018 Mar 17.

17.

Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.

Gill SC, Lim NM, Grinaway PB, Rustenburg AS, Fass J, Ross GA, Chodera JD, Mobley DL.

J Phys Chem B. 2018 May 31;122(21):5579-5598. doi: 10.1021/acs.jpcb.7b11820. Epub 2018 Mar 12.

18.

Atomic Radius and Charge Parameter Uncertainty in Biomolecular Solvation Energy Calculations.

Yang X, Lei H, Gao P, Thomas DG, Mobley DL, Baker NA.

J Chem Theory Comput. 2018 Feb 13;14(2):759-767. doi: 10.1021/acs.jctc.7b00905. Epub 2018 Jan 29.

19.

Collaborative routes to clarifying the murky waters of aqueous supramolecular chemistry.

Cremer PS, Flood AH, Gibb BC, Mobley DL.

Nat Chem. 2017 Dec 19;10(1):8-16. doi: 10.1038/nchem.2894. Review.

20.

Synthesis facilitates an understanding of the structural basis for translation inhibition by the lissoclimides.

Könst ZA, Szklarski AR, Pellegrino S, Michalak SE, Meyer M, Zanette C, Cencic R, Nam S, Voora VK, Horne DA, Pelletier J, Mobley DL, Yusupova G, Yusupov M, Vanderwal CD.

Nat Chem. 2017 Nov;9(11):1140-1149. doi: 10.1038/nchem.2800. Epub 2017 Jul 3.

21.

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Matos GDR, Kyu DY, Loeffler HH, Chodera JD, Shirts MR, Mobley DL.

J Chem Eng Data. 2017 May 11;62(5):1559-1569. doi: 10.1021/acs.jced.7b00104. Epub 2017 Apr 24.

22.

Erratum to: 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.

J Comput Aided Mol Des. 2017 Aug;31(8):777. doi: 10.1007/s10822-017-0043-4. No abstract available.

23.

A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations.

Abel R, Wang L, Mobley DL, Friesner RA.

Curr Top Med Chem. 2017;17(23):2577-2585. doi: 10.2174/1568026617666170414142131. Review.

24.

Predicting Binding Free Energies: Frontiers and Benchmarks.

Mobley DL, Gilson MK.

Annu Rev Biophys. 2017 May 22;46:531-558. doi: 10.1146/annurev-biophys-070816-033654. Epub 2017 Apr 7. Review.

25.

Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.

Gosink LJ, Overall CC, Reehl SM, Whitney PD, Mobley DL, Baker NA.

J Phys Chem B. 2017 Apr 20;121(15):3458-3472. doi: 10.1021/acs.jpcb.6b09198. Epub 2017 Jan 4.

26.

Multiple binding modes of ibuprofen in human serum albumin identified by absolute binding free energy calculations.

Evoli S, Mobley DL, Guzzi R, Rizzuti B.

Phys Chem Chem Phys. 2016 Nov 30;18(47):32358-32368.

27.

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.

J Comput Aided Mol Des. 2017 Jan;31(1):147-161. doi: 10.1007/s10822-016-9977-1. Epub 2016 Oct 27. Erratum in: J Comput Aided Mol Des. 2017 Jul 27;:.

28.

Measuring experimental cyclohexane-water distribution coefficients for the SAMPL5 challenge.

Rustenburg AS, Dancer J, Lin B, Feng JA, Ortwine DF, Mobley DL, Chodera JD.

J Comput Aided Mol Des. 2016 Nov;30(11):945-958. doi: 10.1007/s10822-016-9971-7. Epub 2016 Oct 7.

29.

Blind prediction of cyclohexane-water distribution coefficients from the SAMPL5 challenge.

Bannan CC, Burley KH, Chiu M, Shirts MR, Gilson MK, Mobley DL.

J Comput Aided Mol Des. 2016 Nov;30(11):927-944. doi: 10.1007/s10822-016-9954-8. Epub 2016 Sep 27.

30.

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.

J Comput Aided Mol Des. 2017 Jan;31(1):1-19. doi: 10.1007/s10822-016-9974-4. Epub 2016 Sep 22. Review.

31.

Sensitivity in Binding Free Energies Due to Protein Reorganization.

Lim NM, Wang L, Abel R, Mobley DL.

J Chem Theory Comput. 2016 Sep 13;12(9):4620-31. doi: 10.1021/acs.jctc.6b00532. Epub 2016 Aug 16.

32.

Calculating Partition Coefficients of Small Molecules in Octanol/Water and Cyclohexane/Water.

Bannan CC, Calabró G, Kyu DY, Mobley DL.

J Chem Theory Comput. 2016 Aug 9;12(8):4015-24. doi: 10.1021/acs.jctc.6b00449. Epub 2016 Aug 1.

33.

Using MD Simulations To Calculate How Solvents Modulate Solubility.

Liu S, Cao S, Hoang K, Young KL, Paluch AS, Mobley DL.

J Chem Theory Comput. 2016 Apr 12;12(4):1930-41. doi: 10.1021/acs.jctc.5b00934. Epub 2016 Mar 2.

34.

Correction to 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.

J Chem Theory Comput. 2015 Mar 10;11(3):1347. doi: 10.1021/acs.jctc.5b00154. No abstract available.

35.

A Python tool to set up relative free energy calculations in GROMACS.

Klimovich PV, Mobley DL.

J Comput Aided Mol Des. 2015 Nov;29(11):1007-14. doi: 10.1007/s10822-015-9873-0. Epub 2015 Oct 20.

36.

Is ring breaking feasible in relative binding free energy calculations?

Liu S, Wang L, Mobley DL.

J Chem Inf Model. 2015 Apr 27;55(4):727-35. doi: 10.1021/acs.jcim.5b00057. Epub 2015 Apr 16.

37.

Guidelines for the analysis of free energy calculations.

Klimovich PV, Shirts MR, Mobley DL.

J Comput Aided Mol Des. 2015 May;29(5):397-411. doi: 10.1007/s10822-015-9840-9. Epub 2015 Mar 26.

38.

Predicting the excess solubility of acetanilide, acetaminophen, phenacetin, benzocaine, and caffeine in binary water/ethanol mixtures via molecular simulation.

Paluch AS, Parameswaran S, Liu S, Kolavennu A, Mobley DL.

J Chem Phys. 2015 Jan 28;142(4):044508. doi: 10.1063/1.4906491.

39.

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field.

Wang L, Wu Y, Deng Y, Kim B, Pierce L, Krilov G, Lupyan D, Robinson S, Dahlgren MK, Greenwood J, Romero DL, Masse C, Knight JL, Steinbrecher T, Beuming T, Damm W, Harder E, Sherman W, Brewer M, Wester R, Murcko M, Frye L, Farid R, Lin T, Mobley DL, Jorgensen WL, Berne BJ, Friesner RA, Abel R.

J Am Chem Soc. 2015 Feb 25;137(7):2695-703. doi: 10.1021/ja512751q. Epub 2015 Feb 12.

PMID:
25625324
40.

Box size effects are negligible for solvation free energies of neutral solutes.

Parameswaran S, Mobley DL.

J Comput Aided Mol Des. 2014 Aug;28(8):825-9. doi: 10.1007/s10822-014-9766-7. Epub 2014 Jun 30.

PMID:
24976043
41.

FreeSolv: a database of experimental and calculated hydration free energies, with input files.

Mobley DL, Guthrie JP.

J Comput Aided Mol Des. 2014 Jul;28(7):711-20. doi: 10.1007/s10822-014-9747-x. Epub 2014 Jun 14.

42.

A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration.

Fennell CJ, Wymer KL, Mobley DL.

J Phys Chem B. 2014 Jun 19;118(24):6438-46. doi: 10.1021/jp411529h. Epub 2014 Apr 17.

43.

Blind prediction of solvation free energies from the SAMPL4 challenge.

Mobley DL, Wymer KL, Lim NM, Guthrie JP.

J Comput Aided Mol Des. 2014 Mar;28(3):135-50. doi: 10.1007/s10822-014-9718-2. Epub 2014 Mar 11. Review.

44.

The SAMPL4 host-guest blind prediction challenge: an overview.

Muddana HS, Fenley AT, Mobley DL, Gilson MK.

J Comput Aided Mol Des. 2014 Apr;28(4):305-17. doi: 10.1007/s10822-014-9735-1. Epub 2014 Mar 6. Review.

45.

Blind prediction of HIV integrase binding from the SAMPL4 challenge.

Mobley DL, Liu S, Lim NM, Wymer KL, Perryman AL, Forli S, Deng N, Su J, Branson K, Olson AJ.

J Comput Aided Mol Des. 2014 Apr;28(4):327-45. doi: 10.1007/s10822-014-9723-5. Epub 2014 Mar 5. Review.

46.
47.

Lead optimization mapper: automating free energy calculations for lead optimization.

Liu S, Wu Y, Lin T, Abel R, Redmann JP, Summa CM, Jaber VR, Lim NM, Mobley DL.

J Comput Aided Mol Des. 2013 Sep;27(9):755-70. doi: 10.1007/s10822-013-9678-y. Epub 2013 Sep 26.

48.

Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.

Rocklin GJ, Mobley DL, Dill KA.

J Chem Theory Comput. 2013 Jul 9;9(7):3072-3083.

49.

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.

J Mol Biol. 2013 Nov 15;425(22):4569-83. doi: 10.1016/j.jmb.2013.07.030. Epub 2013 Jul 26.

50.

3-Aryl-3-arylmethoxyazetidines. A new class of high affinity ligands for monoamine transporters.

Thaxton A, Izenwasser S, Wade D, Stevens ED, Mobley DL, Jaber V, Lomenzo SA, Trudell ML.

Bioorg Med Chem Lett. 2013 Aug 1;23(15):4404-7. doi: 10.1016/j.bmcl.2013.05.071. Epub 2013 May 29.

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