G. Andres Cisneros, Ph.D. - Publications

2009-2016 Chemistry Wayne State University, Detroit, MI, United States 
 2016- Chemistry University of North Texas, Denton, TX, United States 
Theoretical Chemistry, Computational Chemistry

70 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Leddin EM, Cisneros GA. Comparison of DNA and RNA substrate effects on TET2 structure. Advances in Protein Chemistry. 117: 91-112. PMID 31564308 DOI: 10.1016/Bs.Apcsb.2019.05.002  0.56
2019 Duke RE, Cisneros GA. Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM. Journal of Molecular Modeling. 25: 307. PMID 31501946 DOI: 10.1007/S00894-019-4194-1  1
2018 Torabifard H, Cisneros GA. Insight into wild-type and T1372E TET2-mediated 5hmC oxidation using QM/MM calculations. Chemical Science. 9: 8433-8445. PMID 30542593 DOI: 10.1039/C8Sc02961J  1
2018 DeNizio JE, Liu MY, Leddin E, Cisneros GA, Kohli RM. Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA. Biochemistry. PMID 30387995 DOI: 10.1021/Acs.Biochem.8B00912  0.36
2018 Silvestrov P, Maier SJ, Fang M, Cisneros GA. DNArCdb: A database of cancer biomarkers in DNA repair genes that includes variants related to multiple cancer phenotypes. Dna Repair. 70: 10-17. PMID 30098577 DOI: 10.1016/J.Dnarep.2018.07.010  1
2018 Gokcan H, Kratz EG, Darden TA, Piquemal JP, Cisneros GA. QM/MM Simulations with the Gaussian Electrostatic Model, A Density-Based Polarizable Potential. The Journal of Physical Chemistry Letters. PMID 29775314 DOI: 10.1021/Acs.Jpclett.8B01412  1
2018 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. Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields. Chemical Science. 9: 956-972. PMID 29732110 DOI: 10.1039/C7Sc04531J  1
2018 Silvestrov P, Cisneros GA. Insights into conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations. Theoretical Chemistry Accounts. 137: 78. DOI: 10.1007/S00214-018-2255-7  1
2017 Torabifard H, Reed L, Berry MT, Hein JE, Menke E, Cisneros GA. Computational and experimental characterization of a pyrrolidinium-based ionic liquid for electrolyte applications. The Journal of Chemical Physics. 147: 161731. PMID 29096446 DOI: 10.1063/1.5004680  1
2017 Torabifard H, Cisneros GA. Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport. Chemical Science. 8: 6230-6238. PMID 28989656 DOI: 10.1039/C7Sc00997F  1
2016 Kratz EG, Duke RE, Cisneros GA. Long-range electrostatic corrections in multipolar/polarizable QM/MM simulations. Theoretical Chemistry Accounts. 135. PMID 28367078 DOI: 10.1007/S00214-016-1923-8  1
2016 Walker AR, Bonomi R, Popov V, Gelovani JG, Andrés Cisneros G. Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies. Journal of Molecular Graphics & Modelling. 71: 211-217. PMID 27939933 DOI: 10.1016/J.Jmgm.2016.10.018  0.32
2016 Liu MY, Torabifard H, Crawford DJ, DeNizio JE, Cao XJ, Garcia BA, Cisneros GA, Kohli RM. Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine. Nature Chemical Biology. PMID 27918559 DOI: 10.1038/Nchembio.2250  1
2016 Zhao L, Rathnayake UM, Dewage SW, Wood WN, Veltri AJ, Cisneros GA, Hendrickson TL. Characterization of Tunnel Mutants Reveals a Catalytic Step in Ammonia Delivery by an Aminoacyl-tRNA Amidotransferase. Febs Letters. PMID 27500385 DOI: 10.1002/1873-3468.12347  1
2016 Cisneros GA, Wikfeldt KT, Ojamäe L, Lu J, Xu Y, Torabifard H, Bartók AP, Csányi G, Molinero V, Paesani F. Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions. Chemical Reviews. PMID 27186804 DOI: 10.1021/Acs.Chemrev.5B00644  1
2016 Kratz EG, Walker AR, Lagardère L, Lipparini F, Piquemal JP, Andrés Cisneros G. LICHEM: A QM/MM program for simulations with multipolar and polarizable force fields. Journal of Computational Chemistry. 37: 1019-29. PMID 26781073 DOI: 10.1002/Jcc.24295  0.64
2015 Bonomi R, Mukhopadhyay U, Shavrin A, Yeh HH, Majhi A, Dewage SW, Najjar A, Lu X, Cisneros GA, Tong WP, Alauddin MM, Liu RS, Mangner TJ, Turkman N, Gelovani JG. Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain. Plos One. 10: e0133512. PMID 26244761 DOI: 10.1371/Journal.Pone.0133512  1
2015 Fang D, Duke RE, Cisneros GA. A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations. The Journal of Chemical Physics. 143: 044103. PMID 26233103 DOI: 10.1063/1.4926652  1
2015 Bellow JA, Yousif M, Fang D, Kratz EG, Cisneros GA, Groysman S. Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OC(t)Bu2Ph]. Inorganic Chemistry. 54: 5624-33. PMID 26043187 DOI: 10.1021/Acs.Inorgchem.5B00795  1
2015 Dewage SW, Cisneros GA. Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB). The Journal of Physical Chemistry. B. 119: 3669-77. PMID 25654336 DOI: 10.1021/Jp5123568  1
2015 Torabifard H, Starovoytov ON, Ren P, Cisneros GA. Development of an AMOEBA water model using GEM distributed multipoles Theoretical Chemistry Accounts. 134. DOI: 10.1007/S00214-015-1702-Y  1
2014 Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. 10: 1361-5. PMID 26580355 DOI: 10.1021/Ct500050P  1
2014 Silvestrov P, Müller TA, Clark KN, Hausinger RP, Cisneros GA. Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1). Journal of Molecular Graphics & Modelling. 54: 123-30. PMID 25459764 DOI: 10.1016/J.Jmgm.2014.10.013  1
2014 Elias AA, Cisneros GA. Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I. Advances in Protein Chemistry and Structural Biology. 96: 39-75. PMID 25443954 DOI: 10.1016/Bs.Apcsb.2014.06.003  1
2014 Fang D, Cisneros GA. Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations. Journal of Chemical Theory and Computation. 10: 5136-5148. PMID 25400523 DOI: 10.1021/Ct500572T  1
2014 Starovoytov ON, Torabifard H, Cisneros GA. Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids. The Journal of Physical Chemistry. B. 118: 7156-66. PMID 24901255 DOI: 10.1021/Jp503347F  1
2014 Chaudret R, Gresh N, Narth C, Lagardère L, Darden TA, Cisneros GA, Piquemal JP. S/G-1: an ab initio force-field blending frozen Hermite Gaussian densities and distributed multipoles. Proof of concept and first applications to metal cations. The Journal of Physical Chemistry. A. 118: 7598-612. PMID 24878003 DOI: 10.1021/Jp5051657  1
2014 Cisneros GA, Karttunen M, Ren P, Sagui C. Classical electrostatics for biomolecular simulations. Chemical Reviews. 114: 779-814. PMID 23981057 DOI: 10.1021/Cr300461D  1
2014 Duke RE, Starovoytov ON, Piquemal JP, Cisneros GA. GEM*: A molecular electronic density-based force field for molecular dynamics simulations Journal of Chemical Theory and Computation. 10: 1361-1365. DOI: 10.1021/ct500050p  1
2014 Swett RJ, Elias A, Miller JA, Dyson GE, Cisneros GA. Corrigendum to "Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S)" [DNA Repair 12 (September (9)) (2013) 733-740] Dna Repair. 15: 60. DOI: 10.1016/J.Dnarep.2014.02.005  1
2014 Fang D, Piquemal JP, Liu S, Cisneros GA. DFT-steric-based energy decomposition analysis of intermolecular interactions Theoretical Chemistry Accounts. 133: 1-14. DOI: 10.1007/S00214-014-1484-7  1
2013 Fang D, Chaudret R, Piquemal JP, Cisneros GA. Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes. Journal of Chemical Theory and Computation. 9: 2156-60. PMID 26583709 DOI: 10.1021/Ct400130B  1
2013 Bellow JA, Fang D, Kovacevic N, Martin PD, Shearer J, Cisneros GA, Groysman S. Novel alkoxide cluster topologies featuring rare seesaw geometry at transition metal centers. Chemistry (Weinheim An Der Bergstrasse, Germany). 19: 12225-8. PMID 23934604 DOI: 10.1002/Chem.201302558  1
2013 Swett RJ, Cisneros GA, Feig AL. Disruption of intrinsic motions as a mechanism for enzyme inhibition. Biophysical Journal. 105: 494-501. PMID 23870270 DOI: 10.1016/J.Bpj.2013.05.031  1
2013 Swett RJ, Elias A, Miller JA, Dyson GE, Andrés Cisneros G. Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S). Dna Repair. 12: 733-40. PMID 23830898 DOI: 10.1016/J.Dnarep.2013.06.001  0.48
2013 Burger SK, Cisneros GA. Efficient optimization of van der Waals parameters from bulk properties. Journal of Computational Chemistry. 34: 2313-9. PMID 23828265 DOI: 10.1002/Jcc.23376  1
2013 Fang D, Lord RL, Cisneros GA. Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB. The Journal of Physical Chemistry. B. 117: 6410-20. PMID 23642148 DOI: 10.1021/Jp403116E  1
2013 Cisneros GA, Babin V, Sagui C. Electrostatics interactions in classical simulations. Methods in Molecular Biology (Clifton, N.J.). 924: 243-70. PMID 23034752 DOI: 10.1007/978-1-62703-017-5_10  1
2013 Chaudret R, Gresh N, Cisneros GA, Scemama A, Piquemal JP. Further refinements of next-generation force fields-Nonempirical localization of off-centered points in molecules Canadian Journal of Chemistry. 91: 804-810. DOI: 10.1139/Cjc-2012-0547  1
2013 Kraskouskaya D, Drewry JA, Duodu E, Burger S, Eaton J, Cisneros GA, Gunning PT. Exploring the structural determinants of selective phosphopeptide recognition using bivalent metal-coordination complexes Medchemcomm. 4: 289-292. DOI: 10.1039/C2Md20342A  1
2013 Fang D, Chaudret R, Piquemal JP, Cisneros GA. Toward a deeper understanding of enzyme reactions using the coupled ELF/NCI analysis: Application to DNA repair enzymes Journal of Chemical Theory and Computation. 9: 2156-2160. DOI: 10.1021/ct400130b  1
2012 Moore JD, Lord RL, Cisneros GA, Allen MJ. Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe. Journal of the American Chemical Society. 134: 17372-5. PMID 23067148 DOI: 10.1021/Ja307098Z  1
2012 Swett R, Cisneros GA, Feig AL. Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition. Plos One. 7: e41518. PMID 22844485 DOI: 10.1371/Journal.Pone.0041518  1
2012 Wu P, Cisneros GA, Hu H, Chaudret R, Hu X, Yang W. Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways. The Journal of Physical Chemistry. B. 116: 6889-97. PMID 22417185 DOI: 10.1021/Jp212643J  1
2012 Graham SE, Syeda F, Cisneros GA. Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I. Biochemistry. 51: 2569-78. PMID 22397306 DOI: 10.1021/Bi201856M  1
2012 Zhao L, Dewage SW, Bell MJ, Chang KM, Fatma S, Joshi N, Silva G, Cisneros GA, Hendrickson TL. The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel. Biochemistry. 51: 273-85. PMID 22229412 DOI: 10.1021/Bi201143X  1
2012 Cisneros GA. Application of gaussian electrostatic model (GEM) distributed multipoles in the AMOEBA force field Journal of Chemical Theory and Computation. 8: 5072-5080. DOI: 10.1021/ct300630u  1
2011 Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Physical Chemistry Chemical Physics : Pccp. 13: 11239-47. PMID 21566841 DOI: 10.1039/C0Cp02550J  0.92
2011 Chaudret R, Cisneros GA, Parisel O, Piquemal JP. Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion. Chemistry (Weinheim An Der Bergstrasse, Germany). 17: 2833-7. PMID 21308813 DOI: 10.1002/Chem.201002978  1
2010 Cisneros GA. DFT study of a model system for the dealkylation step catalyzed by AlkB. Interdisciplinary Sciences, Computational Life Sciences. 2: 70-7. PMID 20640798 DOI: 10.1007/S12539-010-0092-Z  1
2010 Elking DM, Cisneros GA, Piquemal JP, Darden TA, Pedersen LG. Gaussian Multipole Model (GMM). Journal of Chemical Theory and Computation. 6: 190-202. PMID 20209077 DOI: 10.1021/Ct900348B  1
2009 Cisneros GA, Perera L, Schaaper RM, Pedersen LC, London RE, Pedersen LG, Darden TA. Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues. Journal of the American Chemical Society. 131: 1550-6. PMID 19119875 DOI: 10.1021/Ja8082818  0.84
2009 Chaudref R, Ulmera S, Van Severena MC, Gresh N, Pansela O, Cisnerosd GA, Darden TA, Piquemal JP. Progress Towards Accurate Molecular Modeling of Metal Complexes Using Polarizable Force Fields Aip Conference Proceedings. 1102: 185-192. DOI: 10.1063/1.3108373  0.96
2008 Cisneros GA, Tholander SN, Parisel O, Darden TA, Elking D, Perera L, Piquemal JP. Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding. International Journal of Quantum Chemistry. 108: 1905-1912. PMID 19606279 DOI: 10.1002/Qua.21675  1
2008 Cisneros GA, Perera L, García-Díaz M, Bebenek K, Kunkel TA, Pedersen LG. Catalytic mechanism of human DNA polymerase lambda with Mg2+ and Mn2+ from ab initio quantum mechanical/molecular mechanical studies. Dna Repair. 7: 1824-34. PMID 18692600 DOI: 10.1016/J.Dnarep.2008.07.007  1
2007 Gresh N, Cisneros GA, Darden TA, Piquemal JP. Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy. Journal of Chemical Theory and Computation. 3: 1960-1986. PMID 18978934 DOI: 10.1021/Ct700134R  1
2007 Cisneros GA, Elking D, Piquemal JP, Darden TA. Numerical fitting of molecular properties to Hermite Gaussians. The Journal of Physical Chemistry. A. 111: 12049-56. PMID 17973464 DOI: 10.1021/Jp074817R  1
2006 Cisneros GA, Piquemal JP, Darden TA. Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods. The Journal of Chemical Physics. 125: 184101. PMID 17115732 DOI: 10.1063/1.2363374  1
2006 Piquemal JP, Perera L, Cisneros GA, Ren P, Pedersen LG, Darden TA. Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure. The Journal of Chemical Physics. 125: 054511. PMID 16942230 DOI: 10.1063/1.2234774  1
2006 Cisneros GA, Piquemal JP, Darden TA. Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions. The Journal of Physical Chemistry. B. 110: 13682-4. PMID 16836309 DOI: 10.1021/Jp062768X  0.92
2006 Piquemal JP, Cisneros GA, Reinhardt P, Gresh N, Darden TA. Towards a force field based on density fitting. The Journal of Chemical Physics. 124: 104101. PMID 16542062 DOI: 10.1063/1.2173256  1
2006 Cisneros GA, Wang M, Silinski P, Fitzgerald MC, Yang W. Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase. The Journal of Physical Chemistry. A. 110: 700-8. PMID 16405343 DOI: 10.1021/Jp0543328  0.52
2005 Cisneros GA, Piquemal JP, Darden TA. Intermolecular electrostatic energies using density fitting. The Journal of Chemical Physics. 123: 044109. PMID 16095348 DOI: 10.1063/1.1947192  1
2005 Cisneros GA, Liu H, Lu Z, Yang W. Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods. The Journal of Chemical Physics. 122: 114502. PMID 15836224 DOI: 10.1063/1.1860560  1
2004 Liu H, Lu Z, Cisneros GA, Yang W. Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions. The Journal of Chemical Physics. 121: 697-706. PMID 15260596 DOI: 10.1063/1.1759318  1
2004 Cisneros GA, Wang M, Silinski P, Fitzgerald MC, Yang W. The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment. Biochemistry. 43: 6885-92. PMID 15170325 DOI: 10.1021/Bi049943P  1
2003 Cisneros GA, Liu H, Zhang Y, Yang W. Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase. Journal of the American Chemical Society. 125: 10384-93. PMID 12926963 DOI: 10.1021/Ja029672A  1
2003 Goj LA, Cisneros GA, Yang W, Widenhoefer RA. Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization Journal of Organometallic Chemistry. 687: 498-507. DOI: 10.1016/J.Jorganchem.2003.09.046  1
2000 Perez-Marín L, Castro M, Otazo-Sánchez E, Cisneros GA. Density functional study of molecular recognition and reactivity of thiourea derivatives used in sensors for heavy metal polluting cations International Journal of Quantum Chemistry. 80: 609-622.  1
2000 Ascencio-Gutiérrez JA, Pérez-Marín L, Otazo-Sánchez E, Castro M, Contreras-Pulido D, Cisneros GA. Molecular and quantum mechanics calculations for the 1-furoyl-3phenylthiourea as a Pb2+ sensor Afinidad. 57: 180-184.  1
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