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Items: 1 to 20 of 103

1.

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 Nov 7. doi: 10.1007/s10822-018-0168-0. [Epub ahead of print]

PMID:
30406372
2.

SAMPL6: calculation of macroscopic pKa values from ab initio quantum mechanical free energies.

Selwa E, Kenney IM, Beckstein O, Iorga BI.

J Comput Aided Mol Des. 2018 Aug 6. doi: 10.1007/s10822-018-0138-6. [Epub ahead of print]

PMID:
30084080
3.

The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory.

Tielker N, Eberlein L, Güssregen S, Kast SM.

J Comput Aided Mol Des. 2018 Aug 2. doi: 10.1007/s10822-018-0140-z. [Epub ahead of print]

PMID:
30073500
4.

High accuracy quantum-chemistry-based calculation and blind prediction of macroscopic pKa values in the context of the SAMPL6 challenge.

Pracht P, Wilcken R, Udvarhelyi A, Rodde S, Grimme S.

J Comput Aided Mol Des. 2018 Aug 23. doi: 10.1007/s10822-018-0145-7. [Epub ahead of print]

PMID:
30141103
5.

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge.

Prasad S, Huang J, Zeng Q, Brooks BR.

J Comput Aided Mol Des. 2018 Oct 1. doi: 10.1007/s10822-018-0167-1. [Epub ahead of print]

PMID:
30276503
6.

Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge.

Zeng Q, Jones MR, Brooks BR.

J Comput Aided Mol Des. 2018 Aug 20. doi: 10.1007/s10822-018-0150-x. [Epub ahead of print]

PMID:
30128926
7.

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.

J Comput Aided Mol Des. 2007 Dec;21(12):681-91. Epub 2007 Sep 27.

PMID:
17899391
9.

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 15. doi: 10.1007/s10822-018-0169-z. [Epub ahead of print]

PMID:
30324305
10.

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange.

Lee J, Miller BT, Damjanović A, Brooks BR.

J Chem Theory Comput. 2014 Jul 8;10(7):2738-2750. Epub 2014 Jun 3.

11.

In silico prediction of ionization constants of drugs.

Lee PH, Ayyampalayam SN, Carreira LA, Shalaeva M, Bhattachar S, Coselmon R, Poole S, Gifford E, Lombardo F.

Mol Pharm. 2007 Jul-Aug;4(4):498-512. Epub 2007 Jul 13.

PMID:
17629304
12.

pKa determination by ¹H NMR spectroscopy - an old methodology revisited.

Bezençon J, Wittwer MB, Cutting B, Smieško M, Wagner B, Kansy M, Ernst B.

J Pharm Biomed Anal. 2014 May;93:147-55. doi: 10.1016/j.jpba.2013.12.014. Epub 2013 Dec 24.

PMID:
24462329
13.

Microscopic pKa analysis of Glu286 in cytochrome c oxidase (Rhodobacter sphaeroides): toward a calibrated molecular model.

Ghosh N, Prat-Resina X, Gunner MR, Cui Q.

Biochemistry. 2009 Mar 24;48(11):2468-85. doi: 10.1021/bi8021284.

PMID:
19243111
14.

On the active site protonation state in aspartic proteases: implications for drug design.

Sussman F, Villaverde MC, Domínguez JL, Danielson UH.

Curr Pharm Des. 2013;19(23):4257-75. Review.

PMID:
23170891
15.

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.

16.

Extending pKa prediction accuracy: high-throughput pKa measurements to understand pKa modulation of new chemical series.

Milletti F, Storchi L, Goracci L, Bendels S, Wagner B, Kansy M, Cruciani G.

Eur J Med Chem. 2010 Sep;45(9):4270-9. doi: 10.1016/j.ejmech.2010.06.026. Epub 2010 Jun 23.

PMID:
20633962
17.

Acid-base equilibria in rhodopsin: dependence of the protonation state of glu134 on its environment.

Periole X, Ceruso MA, Mehler EL.

Biochemistry. 2004 Jun 8;43(22):6858-64.

PMID:
15170322
18.

Toward Quantitatively Accurate Calculation of the Redox-Associated Acid-Base and Ligand Binding Equilibria of Aquacobalamin.

Johnston RC, Zhou J, Smith JC, Parks JM.

J Phys Chem B. 2016 Aug 4;120(30):7307-18. doi: 10.1021/acs.jpcb.6b02701. Epub 2016 Jul 22.

PMID:
27391132
19.

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.

20.

Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pKa Shifts Provide a Unique Benchmark for Electrostatics Models.

Slocum JD, First JT, Webb LJ.

J Phys Chem B. 2017 Jul 20;121(28):6799-6812. doi: 10.1021/acs.jpcb.7b03935. Epub 2017 Jul 11.

PMID:
28650636

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