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Items: 1 to 20 of 26

1.

Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems.

Zheng L, Chen M, Yang W.

Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20227-32. doi: 10.1073/pnas.0810631106. Epub 2008 Dec 15.

2.

Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies.

Cisneros GA, Perera L, García-Díaz M, Bebenek K, Kunkel TA, Pedersen LG.

DNA Repair (Amst). 2008 Nov 1;7(11):1824-34. doi: 10.1016/j.dnarep.2008.07.007. Epub 2008 Aug 30.

3.

Phosphodiester cleavage in ribonuclease H occurs via an associative two-metal-aided catalytic mechanism.

De Vivo M, Dal Peraro M, Klein ML.

J Am Chem Soc. 2008 Aug 20;130(33):10955-62. doi: 10.1021/ja8005786. Epub 2008 Jul 29.

4.

On the interpretation of the observed linear free energy relationship in phosphate hydrolysis: a thorough computational study of phosphate diester hydrolysis in solution.

Rosta E, Kamerlin SC, Warshel A.

Biochemistry. 2008 Mar 25;47(12):3725-35. doi: 10.1021/bi702106m. Epub 2008 Feb 29.

PMID:
18307312
5.

Structure of human RNase H1 complexed with an RNA/DNA hybrid: insight into HIV reverse transcription.

Nowotny M, Gaidamakov SA, Ghirlando R, Cerritelli SM, Crouch RJ, Yang W.

Mol Cell. 2007 Oct 26;28(2):264-76. Erratum in: Mol Cell. 2007 Nov 9;28(3):513.

6.

The role of metal ions in phosphate ester hydrolysis.

Kamerlin SC, Wilkie J.

Org Biomol Chem. 2007 Jul 7;5(13):2098-108. Epub 2007 May 30.

PMID:
17581653
7.

Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms.

Woodcock HL, Hodoscek M, Brooks BR.

J Phys Chem A. 2007 Jul 5;111(26):5720-8. Epub 2007 Jun 8.

PMID:
17555303
8.

A water-mediated and substrate-assisted catalytic mechanism for Sulfolobus solfataricus DNA polymerase IV.

Wang L, Yu X, Hu P, Broyde S, Zhang Y.

J Am Chem Soc. 2007 Apr 18;129(15):4731-7. Epub 2007 Mar 22.

9.

Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations.

Woodcock HL 3rd, Hodoscek M, Gilbert AT, Gill PM, Schaefer HF 3rd, Brooks BR.

J Comput Chem. 2007 Jul 15;28(9):1485-502.

PMID:
17334987
10.

On the mechanism of hydrolysis of phosphate monoesters dianions in solutions and proteins.

Klähn M, Rosta E, Warshel A.

J Am Chem Soc. 2006 Nov 29;128(47):15310-23.

PMID:
17117884
11.

Advances in methods and algorithms in a modern quantum chemistry program package.

Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, Brown ST, Gilbert AT, Slipchenko LV, Levchenko SV, O'Neill DP, DiStasio RA Jr, Lochan RC, Wang T, Beran GJ, Besley NA, Herbert JM, Lin CY, Van Voorhis T, Chien SH, Sodt A, Steele RP, Rassolov VA, Maslen PE, Korambath PP, Adamson RD, Austin B, Baker J, Byrd EF, Dachsel H, Doerksen RJ, Dreuw A, Dunietz BD, Dutoi AD, Furlani TR, Gwaltney SR, Heyden A, Hirata S, Hsu CP, Kedziora G, Khalliulin RZ, Klunzinger P, Lee AM, Lee MS, Liang W, Lotan I, Nair N, Peters B, Proynov EI, Pieniazek PA, Rhee YM, Ritchie J, Rosta E, Sherrill CD, Simmonett AC, Subotnik JE, Woodcock HL 3rd, Zhang W, Bell AT, Chakraborty AK, Chipman DM, Keil FJ, Warshel A, Hehre WJ, Schaefer HF 3rd, Kong J, Krylov AI, Gill PM, Head-Gordon M.

Phys Chem Chem Phys. 2006 Jul 21;8(27):3172-91. Epub 2006 Jun 12. Review.

PMID:
16902710
12.
13.

A recipe for the computation of the free energy barrier and the lowest free energy path of concerted reactions.

Ensing B, Laio A, Parrinello M, Klein ML.

J Phys Chem B. 2005 Apr 14;109(14):6676-87.

PMID:
16851750
14.

Making and breaking nucleic acids: two-Mg2+-ion catalysis and substrate specificity.

Yang W, Lee JY, Nowotny M.

Mol Cell. 2006 Apr 7;22(1):5-13. Review.

15.

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
16.

Alkaline phosphatase mono- and diesterase reactions: comparative transition state analysis.

Zalatan JG, Herschlag D.

J Am Chem Soc. 2006 Feb 1;128(4):1293-303.

17.

Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.

Nowotny M, Gaidamakov SA, Crouch RJ, Yang W.

Cell. 2005 Jul 1;121(7):1005-16.

18.

Type II restriction endonucleases: structure and mechanism.

Pingoud A, Fuxreiter M, Pingoud V, Wende W.

Cell Mol Life Sci. 2005 Mar;62(6):685-707. Review.

PMID:
15770420
19.

The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase.

Thorpe IF, Brooks CL 3rd.

Proteins. 2004 Nov 15;57(3):444-57.

PMID:
15382243
20.

Models for biological phosphoryl transfer.

Williams NH.

Biochim Biophys Acta. 2004 Mar 11;1697(1-2):279-87. Review.

PMID:
15023368
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