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Items: 1 to 20 of 101

1.

Standard state free energies, not pKas, are ideal for describing small molecule protonation and tautomeric states.

Gunner MR, Murakami T, Rustenburg AS, Işık M, Chodera JD.

J Comput Aided Mol Des. 2020 Feb 12. doi: 10.1007/s10822-020-00280-7. [Epub ahead of print]

PMID:
32052350
2.

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.

3.

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 Oct;32(10):1203-1216. doi: 10.1007/s10822-018-0138-6. Epub 2018 Aug 6.

4.

q-Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides.

Fossat MJ, Pappu RV.

J Phys Chem B. 2019 Aug 15;123(32):6952-6967. doi: 10.1021/acs.jpcb.9b05206. Epub 2019 Aug 7.

PMID:
31362509
5.

pH-Dependent Protonation of the Phl p 6 Pollen Allergen Studied by NMR and cpH-aMD.

Hofer F, Dietrich V, Kamenik AS, Tollinger M, Liedl KR.

J Chem Theory Comput. 2019 Oct 8;15(10):5716-5726. doi: 10.1021/acs.jctc.9b00540. Epub 2019 Sep 12.

6.

pH-dependent pKa values in proteins--a theoretical analysis of protonation energies with practical consequences for enzymatic reactions.

Bombarda E, Ullmann GM.

J Phys Chem B. 2010 Feb 11;114(5):1994-2003. doi: 10.1021/jp908926w.

PMID:
20088566
7.

Rigorous Free Energy Perturbation Approach to Estimating Relative Binding Affinities between Ligands with Multiple Protonation and Tautomeric States.

de Oliveira C, Yu HS, Chen W, Abel R, Wang L.

J Chem Theory Comput. 2019 Jan 8;15(1):424-435. doi: 10.1021/acs.jctc.8b00826. Epub 2018 Dec 26. Erratum in: J Chem Theory Comput. 2019 Oct 8;15(10):5758.

PMID:
30537823
9.

Conformational Dynamics and Binding Free Energies of Inhibitors of BACE-1: From the Perspective of Protonation Equilibria.

Kim MO, Blachly PG, McCammon JA.

PLoS Comput Biol. 2015 Oct 27;11(10):e1004341. doi: 10.1371/journal.pcbi.1004341. eCollection 2015 Oct.

10.

Proton affinity changes driving unidirectional proton transport in the bacteriorhodopsin photocycle.

Onufriev A, Smondyrev A, Bashford D.

J Mol Biol. 2003 Oct 3;332(5):1183-93.

PMID:
14499620
11.

On the pH dependence of protein stability.

Yang AS, Honig B.

J Mol Biol. 1993 May 20;231(2):459-74.

PMID:
8510157
12.

Getting the chemistry right: protonation, tautomers and the importance of H atoms in biological chemistry.

Bax B, Chung CW, Edge C.

Acta Crystallogr D Struct Biol. 2017 Feb 1;73(Pt 2):131-140. doi: 10.1107/S2059798316020283. Epub 2017 Feb 1.

13.

Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pK(a) Calculations.

Dobrev P, Donnini S, Groenhof G, Grubmüller H.

J Chem Theory Comput. 2017 Jan 10;13(1):147-160. doi: 10.1021/acs.jctc.6b00807. Epub 2016 Dec 14.

PMID:
27966355
15.
16.

Assessing the protonation state of drug molecules: the case of aztreonam.

Díaz N, Sordo TL, Suárez D, Méndez R, Villacorta JM, Simón L, Rico M, Jiménez MA.

J Med Chem. 2006 Jun 1;49(11):3235-43.

PMID:
16722641
17.

Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues.

Huang Q, Herrmann A.

Protein Cell. 2012 Mar;3(3):230-8. doi: 10.1007/s13238-012-2035-4. Epub 2012 Mar 31.

18.

Protocols utilizing constant pH molecular dynamics to compute pH-dependent binding free energies.

Kim MO, Blachly PG, Kaus JW, McCammon JA.

J Phys Chem B. 2015 Jan 22;119(3):861-72. doi: 10.1021/jp505777n. Epub 2014 Aug 25.

19.

Theoretical and experimental studies of the isomeric protonation in solution for a prototype aliphatic ring containing two nitrogens.

Nagy PI, Maheshwari A, Kim YW, Messer WS Jr.

J Phys Chem B. 2010 Jan 14;114(1):349-60. doi: 10.1021/jp9082085.

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