Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 111

1.

Effects of system net charge and electrostatic truncation on all-atom constant pH molecular dynamics.

Chen W, Shen JK.

J Comput Chem. 2014 Oct 15;35(27):1986-96. doi: 10.1002/jcc.23713. Epub 2014 Aug 21.

2.

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.

Wallace JA, Shen JK.

J Chem Phys. 2012 Nov 14;137(18):184105. doi: 10.1063/1.4766352.

3.
4.

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water.

Huang Y, Chen W, Wallace JA, Shen J.

J Chem Theory Comput. 2016 Nov 8;12(11):5411-5421. Epub 2016 Oct 24.

PMID:
27709966
5.

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism.

Goh GB, Hulbert BS, Zhou H, Brooks CL 3rd.

Proteins. 2014 Jul;82(7):1319-31. doi: 10.1002/prot.24499. Epub 2014 Jan 15.

6.

Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation.

Reif MM, Oostenbrink C.

J Comput Chem. 2014 Jan 30;35(3):227-43. doi: 10.1002/jcc.23490. Epub 2013 Nov 19.

7.

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer.

Donnini S, Ullmann RT, Groenhof G, Grubm├╝ller H.

J Chem Theory Comput. 2016 Mar 8;12(3):1040-51. doi: 10.1021/acs.jctc.5b01160. Epub 2016 Feb 26.

PMID:
26881315
8.

On the truncation of long-range electrostatic interactions in DNA.

Norberg J, Nilsson L.

Biophys J. 2000 Sep;79(3):1537-53.

9.

Introducing titratable water to all-atom molecular dynamics at constant pH.

Chen W, Wallace JA, Yue Z, Shen JK.

Biophys J. 2013 Aug 20;105(4):L15-7. doi: 10.1016/j.bpj.2013.06.036.

10.
11.

Is the prediction of pKa values by constant-pH molecular dynamics being hindered by inherited problems?

Machuqueiro M, Baptista AM.

Proteins. 2011 Dec;79(12):3437-47. doi: 10.1002/prot.23115. Epub 2011 Aug 30.

PMID:
22072522
12.

Simple and accurate scheme to compute electrostatic interaction: zero-dipole summation technique for molecular system and application to bulk water.

Fukuda I, Kamiya N, Yonezawa Y, Nakamura H.

J Chem Phys. 2012 Aug 7;137(5):054314. doi: 10.1063/1.4739789.

PMID:
22894355
13.

pKa values in proteins determined by electrostatics applied to molecular dynamics trajectories.

Meyer T, Knapp EW.

J Chem Theory Comput. 2015 Jun 9;11(6):2827-40. doi: 10.1021/acs.jctc.5b00123. Epub 2015 May 19.

PMID:
26575575
14.

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

Goh GB, Knight JL, Brooks CL 3rd.

J Phys Chem Lett. 2013 Mar 7;4(5):760-766. Epub 2013 Feb 12.

15.

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics.

Arthur EJ, Yesselman JD, Brooks CL 3rd.

Proteins. 2011 Dec;79(12):3276-86. doi: 10.1002/prot.23195. Epub 2011 Oct 15.

16.
17.

Toward accurate prediction of pKa values for internal protein residues: the importance of conformational relaxation and desolvation energy.

Wallace JA, Wang Y, Shi C, Pastoor KJ, Nguyen BL, Xia K, Shen JK.

Proteins. 2011 Dec;79(12):3364-73. doi: 10.1002/prot.23080. Epub 2011 Jul 11.

PMID:
21748801
18.

Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

Lee J, Miller BT, Brooks BR.

Protein Sci. 2016 Jan;25(1):231-43. doi: 10.1002/pro.2755. Epub 2015 Aug 20.

19.

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, Grubm├╝ller H.

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

PMID:
27966355
20.

Supplemental Content

Support Center