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Results: 1 to 20 of 97

1.

How Accurate Are Transition States from Simulations of Enzymatic Reactions?

Doron D, Kohen A, Nam K, Major DT.

J Chem Theory Comput. 2014 May 13;10(5):1863-1871. Epub 2014 Apr 23.

PMID:
24860275
[PubMed]
2.

Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase.

Garcia-Viloca M, Truhlar DG, Gao J.

Biochemistry. 2003 Nov 25;42(46):13558-75.

PMID:
14622003
[PubMed - indexed for MEDLINE]
3.

Simulations of remote mutants of dihydrofolate reductase reveal the nature of a network of residues coupled to hydride transfer.

Roston D, Kohen A, Doron D, Major DT.

J Comput Chem. 2014 Jul 15;35(19):1411-7. doi: 10.1002/jcc.23629. Epub 2014 May 2.

PMID:
24798860
[PubMed - in process]
4.

Comparison of coupled motions in Escherichia coli and Bacillus subtilis dihydrofolate reductase.

Watney JB, Hammes-Schiffer S.

J Phys Chem B. 2006 May 25;110(20):10130-8.

PMID:
16706474
[PubMed - indexed for MEDLINE]
5.

Reaction rate theory: what it was, where is it today, and where is it going?

Pollak E, Talkner P.

Chaos. 2005 Jun;15(2):26116.

PMID:
16035918
[PubMed - indexed for MEDLINE]
6.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
[PubMed - as supplied by publisher]
7.

Global dynamics and transition state theories: Comparative study of reaction rate constants for gas-phase chemical reactions.

Ju LP, Han KL, Zhang JZ.

J Comput Chem. 2009 Jan 30;30(2):305-16. doi: 10.1002/jcc.21032.

PMID:
18615407
[PubMed]
8.

Transition state theory can be used in studies of enzyme catalysis: lessons from simulations of tunnelling and dynamical effects in lipoxygenase and other systems.

Olsson MH, Mavri J, Warshel A.

Philos Trans R Soc Lond B Biol Sci. 2006 Aug 29;361(1472):1417-32.

PMID:
16873128
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

Billeter SR, Webb SP, Agarwal PK, Iordanov T, Hammes-Schiffer S.

J Am Chem Soc. 2001 Nov 14;123(45):11262-72.

PMID:
11697969
[PubMed - indexed for MEDLINE]
10.

Hybrid schemes based on quantum mechanics/molecular mechanics simulations goals to success, problems, and perspectives.

Ferrer S, Ruiz-Pernía J, Martí S, Moliner V, Tuñón I, Bertrán J, Andrés J.

Adv Protein Chem Struct Biol. 2011;85:81-142. doi: 10.1016/B978-0-12-386485-7.00003-X. Review.

PMID:
21920322
[PubMed - indexed for MEDLINE]
11.

Freezing a single distal motion in dihydrofolate reductase.

Sergi A, Watney JB, Wong KF, Hammes-Schiffer S.

J Phys Chem B. 2006 Feb 9;110(5):2435-41.

PMID:
16471835
[PubMed - indexed for MEDLINE]
12.

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]
13.

Cyclohexane isomerization. Unimolecular dynamics of the twist-boat intermediate.

Kakhiani K, Lourderaj U, Hu W, Birney D, Hase WL.

J Phys Chem A. 2009 Apr 23;113(16):4570-80. doi: 10.1021/jp811208g.

PMID:
19290605
[PubMed]
14.

Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes.

Gao J, Major DT, Fan Y, Lin YL, Ma S, Wong KY.

Methods Mol Biol. 2008;443:37-62. doi: 10.1007/978-1-59745-177-2_3.

PMID:
18446281
[PubMed - indexed for MEDLINE]
15.

[Modeling the transition state of enzyme-catalyzed phosphoryl transfer reaction using QM/MM method].

Re S, Sugita Y.

Yakugaku Zasshi. 2011;131(8):1171-82. Review. Japanese.

PMID:
21804320
[PubMed - indexed for MEDLINE]
Free Article
16.

Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.

Haines BE, Steussy CN, Stauffacher CV, Wiest O.

Biochemistry. 2012 Oct 9;51(40):7983-95. doi: 10.1021/bi3008593. Epub 2012 Sep 25.

PMID:
22971202
[PubMed - indexed for MEDLINE]
Free PMC Article
18.
19.

Preorganization and protein dynamics in enzyme catalysis.

Rajagopalan PT, Benkovic SJ.

Chem Rec. 2002;2(1):24-36. Review.

PMID:
11933259
[PubMed - indexed for MEDLINE]
20.

Importance of polarization in quantum mechanics/molecular mechanics descriptions of electronic excited states: NaI(H2O)n photodissociation dynamics as a case study.

Koch DM, Peslherbe GH.

J Phys Chem B. 2008 Jan 17;112(2):636-49. doi: 10.1021/jp709656z.

PMID:
18183959
[PubMed - indexed for MEDLINE]

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