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Results: 20

1.

Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.

Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL 3rd.

PLoS Comput Biol. 2014 Jul 24;10(7):e1003719. doi: 10.1371/journal.pcbi.1003719. eCollection 2014 Jul.

PMID:
25057988
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Quantum mechanical study of solvent effects in a prototype SN2 reaction in solution: Cl- attack on CH3Cl.

Kuechler ER, York DM.

J Chem Phys. 2014 Feb 7;140(5):054109. doi: 10.1063/1.4863344. Erratum in: J Chem Phys. 2014 Mar 7;140(9):099901.

PMID:
24511924
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Cupric yersiniabactin is a virulence-associated superoxide dismutase mimic.

Chaturvedi KS, Hung CS, Giblin DE, Urushidani S, Austin AM, Dinauer MC, Henderson JP.

ACS Chem Biol. 2014 Feb 21;9(2):551-61. doi: 10.1021/cb400658k. Epub 2013 Dec 11.

PMID:
24283977
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Fundamental reaction pathway for peptide metabolism by proteasome: insights from first-principles quantum mechanical/molecular mechanical free energy calculations.

Wei D, Fang L, Tang M, Zhan CG.

J Phys Chem B. 2013 Oct 31;117(43):13418-34. doi: 10.1021/jp405337v. Epub 2013 Oct 10.

PMID:
24111489
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Fundamental reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of heroin.

Qiao Y, Han K, Zhan CG.

Biochemistry. 2013 Sep 17;52(37):6467-79. doi: 10.1021/bi400709v. Epub 2013 Aug 30.

PMID:
23992153
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

DFT studies of conversion of methyl chloride and three substituted chloromethyl tetrahydrofuran derivatives during reaction with trimethylamine.

Walczak D, Nowacki A.

J Mol Model. 2013 Oct;19(10):4403-17. doi: 10.1007/s00894-013-1940-7. Epub 2013 Aug 6.

PMID:
23918221
[PubMed]
Free PMC Article
7.

Modeling catalytic promiscuity in the alkaline phosphatase superfamily.

Duarte F, Amrein BA, Kamerlin SC.

Phys Chem Chem Phys. 2013 Jul 21;15(27):11160-77. doi: 10.1039/c3cp51179k. Epub 2013 Jun 3.

PMID:
23728154
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Protein engineering for metabolic engineering: current and next-generation tools.

Marcheschi RJ, Gronenberg LS, Liao JC.

Biotechnol J. 2013 May;8(5):545-55. doi: 10.1002/biot.201200371. Epub 2013 Apr 16. Review.

PMID:
23589443
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

DFT studies of the conversion of four mesylate esters during reaction with ammonia.

Nowacki A, Sikora K, Dmochowska B, Wiƛniewski A.

J Mol Model. 2013 Aug;19(8):3015-26. doi: 10.1007/s00894-013-1835-7. Epub 2013 Apr 10.

PMID:
23571822
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Pseudobond parameters for QM/MM studies involving nucleosides, nucleotides, and their analogs.

Chaudret R, Parks JM, Yang W.

J Chem Phys. 2013 Jan 28;138(4):045102. doi: 10.1063/1.4772182.

PMID:
23387624
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Engineering a model protein cavity to catalyze the Kemp elimination.

Merski M, Shoichet BK.

Proc Natl Acad Sci U S A. 2012 Oct 2;109(40):16179-83. doi: 10.1073/pnas.1208076109. Epub 2012 Sep 17.

PMID:
22988064
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Fundamental reaction pathway and free energy profile for inhibition of proteasome by Epoxomicin.

Wei D, Lei B, Tang M, Zhan CG.

J Am Chem Soc. 2012 Jun 27;134(25):10436-50. doi: 10.1021/ja3006463. Epub 2012 Jun 14.

PMID:
22697787
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Investigation of solvent effects on the rate and stereoselectivity of the Henry reaction.

Kostal J, Voutchkova AM, Jorgensen WL.

Org Lett. 2012 Jan 6;14(1):260-3. doi: 10.1021/ol2030394. Epub 2011 Dec 14.

PMID:
22168236
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Conical intersections in solution: formulation, algorithm, and implementation with combined quantum mechanics/molecular mechanics method.

Cui G, Yang W.

J Chem Phys. 2011 May 28;134(20):204115. doi: 10.1063/1.3593390.

PMID:
21639432
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Dipole preserving and polarization consistent charges.

Zhang P, Bao P, Gao J.

J Comput Chem. 2011 Jul 30;32(10):2127-39. doi: 10.1002/jcc.21795. Epub 2011 May 3.

PMID:
21541954
[PubMed - in process]
Free PMC Article
16.

Proton transfer facilitated by ligand binding. An energetic analysis of the catalytic mechanism of Trypanosoma cruzi trans-sialidase.

Pierdominici-Sottile G, Roitberg AE.

Biochemistry. 2011 Feb 8;50(5):836-42. doi: 10.1021/bi101648z. Epub 2011 Jan 11.

PMID:
21162542
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

An exciting but challenging road ahead for computational enzyme design.

Baker D.

Protein Sci. 2010 Oct;19(10):1817-9. doi: 10.1002/pro.481. No abstract available.

PMID:
20717908
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Exploring solvent effects upon the Menshutkin reaction using a polarizable force field.

Acevedo O, Jorgensen WL.

J Phys Chem B. 2010 Jul 1;114(25):8425-30. doi: 10.1021/jp100765v.

PMID:
20527873
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect.

Kostal J, Jorgensen WL.

J Am Chem Soc. 2010 Jun 30;132(25):8766-73. doi: 10.1021/ja1023755.

PMID:
20524660
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water.

Thomas LL, Tirado-Rives J, Jorgensen WL.

J Am Chem Soc. 2010 Mar 10;132(9):3097-104. doi: 10.1021/ja909740y.

PMID:
20148559
[PubMed - indexed for MEDLINE]
Free PMC Article
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