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Items: 1 to 20 of 90

1.

Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.

Fu Z, Li X, Miao Y, Merz KM Jr.

J Chem Theory Comput. 2013 Dec 3;9(3):1686-1693. Epub 2013 Feb 18.

2.

Accurate assessment of the strain energy in a protein-bound drug using QM/MM X-ray refinement and converged quantum chemistry.

Fu Z, Li X, Merz KM Jr.

J Comput Chem. 2011 Sep;32(12):2587-97. doi: 10.1002/jcc.21838. Epub 2011 May 19.

PMID:
21598285
3.

Conformational Analysis of Free and Bound Retinoic Acid.

Fu Z, Li X, Merz KM Jr.

J Chem Theory Comput. 2012 Apr 10;8(4):1436-1448. Epub 2012 Feb 24.

4.

QM/MM refinement and analysis of protein bound retinoic acid.

Li X, Fu Z, Merz KM Jr.

J Comput Chem. 2012 Jan 30;33(3):301-10. doi: 10.1002/jcc.21978. Epub 2011 Nov 23.

5.

Conformational variability of benzamidinium-based inhibitors.

Li X, He X, Wang B, Merz K Jr.

J Am Chem Soc. 2009 Jun 10;131(22):7742-54. doi: 10.1021/ja9010833.

6.

Acetylcholinesterase complexed with bivalent ligands related to huperzine a: experimental evidence for species-dependent protein-ligand complementarity.

Wong DM, Greenblatt HM, Dvir H, Carlier PR, Han YF, Pang YP, Silman I, Sussman JL.

J Am Chem Soc. 2003 Jan 15;125(2):363-73.

PMID:
12517147
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Quantum refinement of protein structures: implementation and application to the red fluorescent protein DsRed.M1.

Hsiao YW, Sanchez-Garcia E, Doerr M, Thiel W.

J Phys Chem B. 2010 Nov 25;114(46):15413-23. doi: 10.1021/jp108095n. Epub 2010 Oct 26.

PMID:
20977248
11.

Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.

Yu N, Yennawar HP, Merz KM Jr.

Acta Crystallogr D Biol Crystallogr. 2005 Mar;61(Pt 3):322-32. Epub 2005 Feb 24.

PMID:
15735343
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14.

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.

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Neuroprotective effects of donepezil through inhibition of GSK-3 activity in amyloid-beta-induced neuronal cell death.

Noh MY, Koh SH, Kim Y, Kim HY, Cho GW, Kim SH.

J Neurochem. 2009 Mar;108(5):1116-25. doi: 10.1111/j.1471-4159.2008.05837.x. Epub 2009 Jan 23.

17.

QM/MM X-ray refinement of zinc metalloenzymes.

Li X, Hayik SA, Merz KM Jr.

J Inorg Biochem. 2010 May;104(5):512-22. doi: 10.1016/j.jinorgbio.2009.12.022. Epub 2010 Jan 7.

18.

Ab initio study of hydrogen-bond formation between aliphatic and phenolic hydroxy groups and selected amino acid side chains.

Nagy PI, Erhardt PW.

J Phys Chem A. 2008 May 8;112(18):4342-54. doi: 10.1021/jp7108847. Epub 2008 Mar 29.

PMID:
18373368
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