Shelley JC - Search Results

1

Epik: pK_a and Protonation State Prediction through Machine Learning.

Johnston RC, Yao K, Kaplan Z, Chelliah M, Leswing K, Seekins S, Watts S, Calkins D, Chief Elk J, Jerome SV, Repasky MP, Shelley JC. Johnston RC, et al. Among authors: shelley jc. J Chem Theory Comput. 2023 Apr 25;19(8):2380-2388. doi: 10.1021/acs.jctc.3c00044. Epub 2023 Apr 6. J Chem Theory Comput. 2023. PMID: 37023332

2

Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution.

Greenwood JR, Calkins D, Sullivan AP, Shelley JC. Greenwood JR, et al. Among authors: shelley jc. J Comput Aided Mol Des. 2010 Jun;24(6-7):591-604. doi: 10.1007/s10822-010-9349-1. Epub 2010 Mar 31. J Comput Aided Mol Des. 2010. PMID: 20354892

3

Comments on the article "Evaluation of pK(a) estimation methods on 211 druglike compounds".

Shelley JC, Calkins D, Sullivan AP. Shelley JC, et al. J Chem Inf Model. 2011 Jan 24;51(1):102-4. doi: 10.1021/ci100332m. Epub 2010 Dec 7. J Chem Inf Model. 2011. PMID: 21138320

4

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W. Shivakumar D, et al. J Chem Theory Comput. 2010 May 11;6(5):1509-19. doi: 10.1021/ct900587b. Epub 2010 Apr 14. J Chem Theory Comput. 2010. PMID: 26615687

5

A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution.

Shelley MY, Selvan ME, Zhao J, Babin V, Liao C, Li J, Shelley JC. Shelley MY, et al. Among authors: shelley jc. J Chem Theory Comput. 2017 Aug 8;13(8):3881-3897. doi: 10.1021/acs.jctc.7b00071. Epub 2017 Jul 11. J Chem Theory Comput. 2017. PMID: 28636825 Free PMC article.

6

Epik: a software program for pK( a ) prediction and protonation state generation for drug-like molecules.

Shelley JC, Cholleti A, Frye LL, Greenwood JR, Timlin MR, Uchimaya M. Shelley JC, et al. J Comput Aided Mol Des. 2007 Dec;21(12):681-91. doi: 10.1007/s10822-007-9133-z. Epub 2007 Sep 27. J Comput Aided Mol Des. 2007. PMID: 17899391

7

Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.

Wang L, Deng Y, Knight JL, Wu Y, Kim B, Sherman W, Shelley JC, Lin T, Abel R. Wang L, et al. Among authors: shelley jc. J Chem Theory Comput. 2013 Feb 12;9(2):1282-93. doi: 10.1021/ct300911a. Epub 2013 Jan 30. J Chem Theory Comput. 2013. PMID: 26588769

8

Macrocycle conformational sampling with MacroModel.

Watts KS, Dalal P, Tebben AJ, Cheney DL, Shelley JC. Watts KS, et al. Among authors: shelley jc. J Chem Inf Model. 2014 Oct 27;54(10):2680-96. doi: 10.1021/ci5001696. Epub 2014 Oct 6. J Chem Inf Model. 2014. PMID: 25233464

9

Calculating Apparent pK_a Values of Ionizable Lipids in Lipid Nanoparticles.

Hamilton NB, Arns S, Shelley M, Bechis I, Shelley JC. Hamilton NB, et al. Among authors: shelley jc. Mol Pharm. 2024 Dec 10. doi: 10.1021/acs.molpharmaceut.4c00426. Online ahead of print. Mol Pharm. 2024. PMID: 39655829

10

ConfGen: a conformational search method for efficient generation of bioactive conformers.

Watts KS, Dalal P, Murphy RB, Sherman W, Friesner RA, Shelley JC. Watts KS, et al. Among authors: shelley jc. J Chem Inf Model. 2010 Apr 26;50(4):534-46. doi: 10.1021/ci100015j. J Chem Inf Model. 2010. PMID: 20373803

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