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Results: 1 to 20 of 166

1.

Paradynamics: an effective and reliable model for ab initio QM/MM free-energy calculations and related tasks.

Plotnikov NV, Kamerlin SC, Warshel A.

J Phys Chem B. 2011 Jun 23;115(24):7950-62. doi: 10.1021/jp201217b. Epub 2011 May 27.

PMID:
21618985
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Towards accurate ab initio QM/MM calculations of free-energy profiles of enzymatic reactions.

Rosta E, Klähn M, Warshel A.

J Phys Chem B. 2006 Feb 16;110(6):2934-41.

PMID:
16471904
[PubMed - indexed for MEDLINE]
3.

Exploring, refining, and validating the paradynamics QM/MM sampling.

Plotnikov NV, Warshel A.

J Phys Chem B. 2012 Aug 30;116(34):10342-56. doi: 10.1021/jp304678d. Epub 2012 Aug 21.

PMID:
22853800
[PubMed - indexed for MEDLINE]
4.

Accelerating QM/MM free energy calculations: representing the surroundings by an updated mean charge distribution.

Rosta E, Haranczyk M, Chu ZT, Warshel A.

J Phys Chem B. 2008 May 8;112(18):5680-92. doi: 10.1021/jp711496y. Epub 2008 Apr 16.

PMID:
18412414
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Quantifying free energy profiles of proton transfer reactions in solution and proteins by using a diabatic FDFT mapping.

Xiang Y, Warshel A.

J Phys Chem B. 2008 Jan 24;112(3):1007-15. doi: 10.1021/jp076931f. Epub 2008 Jan 1.

PMID:
18166038
[PubMed - indexed for MEDLINE]
6.

Quantum mechanics/molecular mechanics minimum free-energy path for accurate reaction energetics in solution and enzymes: sequential sampling and optimization on the potential of mean force surface.

Hu H, Lu Z, Parks JM, Burger SK, Yang W.

J Chem Phys. 2008 Jan 21;128(3):034105. doi: 10.1063/1.2816557.

PMID:
18205486
[PubMed - indexed for MEDLINE]
7.
8.

Quantifying the mechanism of phosphate monoester hydrolysis in aqueous solution by evaluating the relevant ab initio QM/MM free-energy surfaces.

Plotnikov NV, Prasad BR, Chakrabarty S, Chu ZT, Warshel A.

J Phys Chem B. 2013 Oct 24;117(42):12807-19. doi: 10.1021/jp4020146. Epub 2013 May 30.

PMID:
23601038
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies.

Kamerlin SC, Haranczyk M, Warshel A.

J Phys Chem B. 2009 Feb 5;113(5):1253-72. doi: 10.1021/jp8071712. Review.

PMID:
19055405
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions.

Klähn M, Braun-Sand S, Rosta E, Warshel A.

J Phys Chem B. 2005 Aug 18;109(32):15645-50.

PMID:
16852982
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Frozen density functional free energy simulations of redox proteins: computational studies of the reduction potential of plastocyanin and rusticyanin.

Olsson MH, Hong G, Warshel A.

J Am Chem Soc. 2003 Apr 30;125(17):5025-39.

PMID:
12708852
[PubMed - indexed for MEDLINE]
12.

Ab initio calculations of free energy barriers for chemical reactions in solution: proton transfer in [FHF]-.

Muller RP, Warshel A.

Pac Symp Biocomput. 1996:524-38.

PMID:
9390256
[PubMed - indexed for MEDLINE]
13.

Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods.

Hu H, Yang W.

Annu Rev Phys Chem. 2008;59:573-601. doi: 10.1146/annurev.physchem.59.032607.093618. Review.

PMID:
18393679
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

QM/MM Minimum Free Energy Path: Methodology and Application to Triosephosphate Isomerase.

Hu H, Lu Z, Yang W.

J Chem Theory Comput. 2007 Mar;3(2):390-406.

PMID:
19079734
[PubMed]
Free PMC Article
15.

Proceedings of the Second Workshop on Theory meets Industry (Erwin-Schrödinger-Institute (ESI), Vienna, Austria, 12-14 June 2007).

Hafner J.

J Phys Condens Matter. 2008 Feb 13;20(6):060301. doi: 10.1088/0953-8984/20/06/060301. Epub 2008 Jan 24.

PMID:
21693862
[PubMed]
16.

Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method.

Zeng X, Hu H, Hu X, Yang W.

J Chem Phys. 2009 Apr 28;130(16):164111. doi: 10.1063/1.3120605.

PMID:
19405565
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Fragment quantum mechanical calculation of proteins and its applications.

He X, Zhu T, Wang X, Liu J, Zhang JZ.

Acc Chem Res. 2014 Sep 16;47(9):2748-57. doi: 10.1021/ar500077t. Epub 2014 May 22.

PMID:
24851673
[PubMed - in process]
18.

Recent advances in QM/MM free energy calculations using reference potentials.

Duarte F, Amrein BA, Blaha-Nelson D, Kamerlin SC.

Biochim Biophys Acta. 2014 Jul 16. pii: S0304-4165(14)00246-3. doi: 10.1016/j.bbagen.2014.07.008. [Epub ahead of print] Review.

PMID:
25038480
[PubMed - as supplied by publisher]
Free Article
19.

Reductive half-reaction of aldehyde oxidoreductase toward acetaldehyde: Ab initio and free energy quantum mechanical/molecular mechanical calculations.

Dieterich JM, Werner HJ, Mata RA, Metz S, Thiel W.

J Chem Phys. 2010 Jan 21;132(3):035101. doi: 10.1063/1.3280164.

PMID:
20095751
[PubMed - indexed for MEDLINE]
20.

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