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Items: 1 to 20 of 65

1.

Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol.

Walker AR, Baddam N, Cisneros GA.

J Phys Chem B. 2019 Apr 18;123(15):3267-3271. doi: 10.1021/acs.jpcb.9b01694. Epub 2019 Apr 4.

PMID:
30912946
2.

LICHEM 1.1: Recent Improvements and New Capabilities.

Gökcan H, Vázquez-Montelongo EA, Cisneros GA.

J Chem Theory Comput. 2019 May 14;15(5):3056-3065. doi: 10.1021/acs.jctc.9b00028. Epub 2019 Apr 2.

PMID:
30908049
3.

Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations.

Torabifard H, Cisneros GA.

Chem Sci. 2018 Sep 11;9(44):8433-8445. doi: 10.1039/c8sc02961j. eCollection 2018 Nov 28.

4.

Selectivity and Promiscuity in TET-Mediated Oxidation of 5-Methylcytosine in DNA and RNA.

DeNizio JE, Liu MY, Leddin EM, Cisneros GA, Kohli RM.

Biochemistry. 2019 Feb 5;58(5):411-421. doi: 10.1021/acs.biochem.8b00912. Epub 2018 Nov 14.

PMID:
30387995
5.

Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF₄].

Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA.

Molecules. 2018 Oct 31;23(11). pii: E2830. doi: 10.3390/molecules23112830.

6.

Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant.

Gahlon HL, Walker AR, Cisneros GA, Lamers MH, Rueda DS.

Phys Chem Chem Phys. 2018 Oct 31;20(42):26892-26902. doi: 10.1039/c8cp04112a.

7.

DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes.

Silvestrov P, Maier SJ, Fang M, Cisneros GA.

DNA Repair (Amst). 2018 Oct;70:10-17. doi: 10.1016/j.dnarep.2018.07.010. Epub 2018 Jul 31.

PMID:
30098577
8.

Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses.

Lohrman J, Vázquez-Montelongo EA, Pramanik S, Day VW, Hix MA, Bowman-James K, Cisneros GA.

Inorg Chem. 2018 Aug 20;57(16):9775-9778. doi: 10.1021/acs.inorgchem.8b00627. Epub 2018 Aug 8.

PMID:
30088923
9.

Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations.

Silvestrov P, Cisneros GA.

Theor Chem Acc. 2018 Jun;137. pii: 78. Epub 2018 May 12.

PMID:
30078993
10.

Characterization of Nine Cancer-Associated Variants in Human DNA Polymerase κ.

Antczak NM, Walker AR, Stern HR, Leddin EM, Palad C, Coulther TA, Swett RJ, Cisneros GA, Beuning PJ.

Chem Res Toxicol. 2018 Aug 20;31(8):697-711. doi: 10.1021/acs.chemrestox.8b00055. Epub 2018 Jul 30.

PMID:
30004685
11.

QM/MM Simulations with the Gaussian Electrostatic Model: A Density-based Polarizable Potential.

Gökcan H, Kratz E, Darden TA, Piquemal JP, Cisneros GA.

J Phys Chem Lett. 2018 Jun 7;9(11):3062-3067. doi: 10.1021/acs.jpclett.8b01412. Epub 2018 May 23.

PMID:
29775314
12.

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields.

Lagardère L, Jolly LH, Lipparini F, Aviat F, Stamm B, Jing ZF, Harger M, Torabifard H, Cisneros GA, Schnieders MJ, Gresh N, Maday Y, Ren PY, Ponder JW, Piquemal JP.

Chem Sci. 2017 Nov 27;9(4):956-972. doi: 10.1039/c7sc04531j. eCollection 2018 Jan 28.

13.

Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] in EMD and NEMD.

Blanco-Díaz EG, Vázquez-Montelongo EA, Cisneros GA, Castrejón-González EO.

J Chem Phys. 2018 Feb 7;148(5):054303. doi: 10.1063/1.5017987.

PMID:
29421909
14.

Molecular dynamics investigation of water-exchange reactions on lanthanide ions in water/1-ethyl-3-methylimidazolium trifluoromethylsufate ([EMIm][OTf]).

Tu YJ, Lin Z, Allen MJ, Cisneros GA.

J Chem Phys. 2018 Jan 14;148(2):024503. doi: 10.1063/1.4997008.

PMID:
29331119
15.

Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations.

Liyanage PS, Walker AR, Brenlla A, Cisneros GA, Romano LJ, Rueda D.

Sci Rep. 2017 Dec 12;7(1):17383. doi: 10.1038/s41598-017-17643-0.

16.

Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications.

Torabifard H, Reed L, Berry MT, Hein JE, Menke E, Cisneros GA.

J Chem Phys. 2017 Oct 28;147(16):161731. doi: 10.1063/1.5004680.

PMID:
29096446
17.

Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport.

Torabifard H, Cisneros GA.

Chem Sci. 2017 Sep 1;8(9):6230-6238. doi: 10.1039/c7sc00997f. Epub 2017 Jul 5.

18.

Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants.

Walker AR, Cisneros GA.

Chem Res Toxicol. 2017 Nov 20;30(11):1922-1935. doi: 10.1021/acs.chemrestox.7b00161. Epub 2017 Sep 15.

19.

Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations.

Kratz EG, Duke RE, Cisneros GA.

Theor Chem Acc. 2016 Jul;135(7). pii: 166. doi: 10.1007/s00214-016-1923-8. Epub 2016 Jun 17.

20.

Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine.

Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM.

Nat Chem Biol. 2017 Feb;13(2):181-187. doi: 10.1038/nchembio.2250. Epub 2016 Dec 5.

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