Cisneros Research Group

The University of Texas at Dallas

  1. Joon P., Hermann G.K. Roy A., Shumate C.K., Cisneros G.A., Yin W.Y., “An interaction network in the polymerase active site is a prerequisite for Watson-Crick base pairing in Pol Gamma”, Science Advances, accepted, 2024.

  2. Maghsoud Y., Roy A., Leddin E.M.,, Cisneros G.A., “Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase kappa”, ChemRxiv, 2024.

  3. Nochebuena J., Simmonett A., Cisneros G.A., “Seamless integration of GEM, a density based-force field, for QM/MM simulations via LICHEM, Psi4 and Tinker-HP”, ChemRxiv, DOI: 10.26434/chemrxiv-2024-8k45x, 2024.

  4. Chatterjee S., Nochebuena J., Cisneros G.A., “Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity”, ChemRxiv, DOI: 10.26434/chemrxiv-2024-ngcmn, 2024.

  5. Nochebuena J., Liu S., Cisneros G.A., “Relative Cooperativity in Neutral and Charged Molecular Clusters Using QM/MM Calculations”, J. Chem. Phys., DOI: 10.1063/5.0203020, 2024.

  6. Debnath T., Cisneros G.A., “Investigation of the Stability of D5SIC-DNAM-Incorporated DNA duplex in Taq Polymerase Binary system: A Systematic Classical MD Approach, Phys. Chem. Chem. Phys., 26, 7287-7295, 2024.

  7. Debnath T., Cisneros G.A., “Investigation of Dynamical flexibility of D5SIC-DNAM inside DNA duplex in Aqueous Solution: A Systematic Classical MD Approach”, Phys. Chem. Chem. Phys., 26, 7435-7445, 2024.

  8. Arora N., Debnath T., Senarathna M., Roske I., Cisneros G.A., Smaldone R., “Rapid, High-Capacity Adsorption of Iodine from Aqueous Environments with Amide Functionalized Covalent Organic Frameworks”, Chem. Sci., DOI: 10.1039/D3SC06004G, 2024.

  9. Case D.A., Aktulga H.M., Belfon K., Cerutti D.S., Cisneros G.A., Cruzeiro V.W.D., Forouzesh N., Giese T.J., Götz A.W., Gohlke H., Izadi S., Kasavajhala K., Kaymak M.C., King E., Kurtzman T., Lee T.-S., Li P., Liu J., Luchko T., Luo R., Manathunga M., Machado M.R., Nguyen H.M., O’Hearn K.A., Onufriev A., Pan F., Pantano S., Qi R., Rahnamoun A., Risheh A., Schott-Verdugo S., Shajan A., Swails J., Wang J., Wei H., Wu X., Wu Y., Zhang S., Zhao S., Zhu Q., Cheatham, III T.T., Roe D.R., Roitberg A., Simmerling C., York D.M., Nagan M.C., Merz, Jr. K.M., “AmberTools”, J. Chem. Inf. Model., DOI: 10.1021/acs.jcim.3c01153, 2023.

  10. Fage C.D., Passmore M., Tatman B.P., Smith H.G., Jian S., Dissanayake U.C., Cisneros G.A., Challis G.L., Lewandowski J.R., Jenner M., “Molecular basis for short-chain thioester hydrolysis by acyl hydrolase domains in trans-acyltransferase polyketide synthases”, BioRxiv, DOI:10.1101/2023.08.11.552765 , 2023.

  11. Nochebuena J., Piquemal J.-P., Liu S., Cisneros G.A., “Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-Polarizable Force Fields”, J. Chem. Theo. Comput, DOI: 10.1021/acs.jctc.3c00762, 2023.

  12. Loo C.E., Hix M.A., Wang T., Cisneros G.A., Kohli R.M., “Revealing drivers for carboxy-S-adenosyl-L-methionine use by neomorphic variants of a DNA methyltransferase”, ACS Chem. Bio., 18, 2224-2232, 2023.

  13. Arche P.D.E., Chatterjee S., Talukder M.M., Miller J.T., Cue J.M.O., Udamulle Gedara C.M., Lord R., Biewer M.C., Cisneros G.A., Stefan M.C., “Regioselective Direct C−H Bond (Hetero)arylation of Thiazoles Enabled by a Novel Iminopyridine-Based α‐Diimine Nickel(II) Complex Evaluated by DFT Studies”, J. Org. Chem., 88, 12319-12382, 2023.

  14. Maghsoud Y., Dong C., Cisneros G.A. “Investigation of the Inhibition Mechanism of Xanthine Oxidoreductase by Oxipurinol: A Computational Study”, J. Chem. Inf. Model., 63, 4190-4206, 2023.

  15. Maghsoud Y., Jayasinghe-Arachchige V.M., Kumari P., Cisneros G.A., Liu J., “Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate off-Target Effects”, J. Chem. Inf. Model, DOI:10.1021/acs.jcim.3c01284, 2023.

  16. Lee J., Guo H.-F., Maghsoud Y., Vazquez-Montelongo E.A., Jing Z., Wang S., Sammons R.M., Cho E.J., Ren P., Cisneros G.A., Kurie J.M., Dalby K.N., “Unleashing the Potential of 1,3-Diketone Analogues as Selective LH2 Inhibitors”, ACS Med. Chem. Lett., 14, 1396-1403, 2023

  17. Maghsoud Y., Dong C., Cisneros G.A. “Computational Characterization of the Inhibition Mechanism of Xanthine Oxidoreductase by Topiroxostat”, ACS Catalysis, 13, 6023-6043, 2023.

  18. Berger M.B., Cisneros G.A. “Distal Mutations in the Beta-clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity”, J. Am. Chem. Soc., 145, 3478-3490, 2023.

  19. Vazquez-Cervantes J.E., Cisneros G.A. “Development of Imidazolium-Based Parameters for AMOEBA-IL”, J. Phys. Chem. B, 127, 5481-5493, 2023.

  20. Maghsoud Y., Vazquez-Montelongo E.A., Yang X., Liu C., Jing Z., Lee J., Harger M., Smith A.K., Espinoza M., Guo H.-F., Kurie J.M., Dalby K.N., Ren P., Cisneros G.A. “Computational Investigation of a Series of Small Molecules as Lead Compounds for Lysyl hydroxylase-2 (LH2) Inhibition”, J. Chem. Inf. Model, 63, 986-1001, 2023.

  21. Mondragon-Solorzano G., Sandoval-Lira J., Nochebuena J., Cisneros G.A., Barroso-Flores J., “Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of Blastochloris viridis’ Light Harvesting 1-Reaction Center Complex”, J. Chem. Theo. Comp., 18, 4555-4564, 2022.

  22. Yeaton A., Cayanan G., Loghavi S., Dolgalev I., Leddin E.M., Loo C., Torabifard H., Nicolet D., Wang J., Corrigan K., Paraskevopoulou V., Starczynowski D., Wang E., Abdel-Wahab O., Viny A., Stone R., Byrd J., Guryanova O., Kohli R., Cisneros G.A., Tsirigos A., Eisfeld A.-K., Aifantis I, Guillamot M., “The impact of inflammation-induced tumor plasticity during myeloid transformation”, Canc. Disc., 12, 2392-2413, 2022.

  23. Simonin-Wilmer I., Ossio R., Leddin E., Harland M., Pooley K.A., Martil de la Garza M.G., Obolenski S., Hewinson J., Wong C.C., Iyer V., Taylor J.C., Newton-Bishop J.A., Bishop D.T., Cisneros G.A., Iles M.M, Adams D.J., Robles-Espinoza C.D. “Population-based analysis of POT1 variants in a cutaneous melanoma case-control cohort”, J. Med. Genetics, DOI:10.1136/jmg-2022-108776, 2022.

  24. Nochebuena J., Cisneros G.A. “Polarizable MD and QM/MM Investigation of Acrylamide-based Leads to Target the Main Protease of SARS-CoV-2”, J. Chem. Phys., 157, 185101, 2022.

  25. Li A.W.H., Zabrady K., Bainbridge L.J., Zabrady M., Naseem-Khan S., Berger M.B., Kolesar P., Cisneros G.A., Doherty, A.J. “Molecular basis for the initiation of DNA primer synthesis”, Nature, 605, 767-773, 2022.

  26. Naseem-Khan S., Berger M.B., Leddin E.M., Maghsoud Y., Cisneros G.A. “Impact of Remdesivir Incorporation Along the Primer Strand on SARS-CoV-2 RNA-dependent RNA polymerase”, J. Chem. Inf. Model., 62, 2456-2465, 2022.

  27. Naseem-Khan S., Lagardere L., Narth C., Cisneros G.A., Ren P., Gresh N., Piquemal J.-P. “Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: I. Enabling Condensed Phase Molecular Dynamics Simulations”, J. Chem. Theo. Comp., 18, 3607-3621, 2022.

  28. Ravishankar K., Jiang X., Leddin E.M., Morcos, F., Cisneros G.A. “Computational Compensatory Mutation Discovery Approach: Predicting a PARP1 Variant Rescue Mutation”, Biophys J., 121, 3663-3673, 2022.

  29. Naseem-Khan S., Piquemal J.–P., Cisneros G.A. “Improvement of the Gaussian Electrostatic Model by Separate Fitting of Coulomb and Exchange-Repulsion Densities and Implementation of a new Dispersion term”, J. Chem. Phys., 155, 194103, 2021.

  30. Berger M.B., Walker A.R., Vazquez-Montelongo E.A., Cisneros G.A. “Computational Investigations of Selected Enzymes From Two Iron and α-ketoglutarate-Dependent Families”, Phys. Chem. Chem. Phys, 23, 22227-22240, 2021.

  31. Gaba A., Hix M.A., Suhail S., Flath B., Boysan B., Williams D.R., Pelletier T., Emerman M., Morcos F., Cisneros G.A., Chelico L. “Divergence in dimerization and activity of primate APOBEC3C”, J. Mol. Bio., DOI: 10.1016/j.jmb.2021.167306, 2021.

  32. Nochebuena J., Quintanar L., Vela A., Cisneros G.A. “Structural and Electronic Analysis of the Octarepeat Region of Prion Protein with Four Cu(II) by Polarizable MD and QM/MM Simulations”, Phys. Chem. Chem. Phys, 23, 21569-21578, 2021.

  33. Hix M.A., Leddin E.M., Cisneros G.A. “Combining Evolutionary Conservation and Quantum Topological Analyses to Determine QM Subsystems for Biomolecular QM/MM Simulations”, J. Chem. Theo. Comp., 17, 4524-4537, 2021.

  34. Nochebuena J., Naseem-Khan S., Cisneros G.A. “Development and Application of Quantum Mechanics/Molecular Mechanics Methods with Advanced Polarizable Potentials”, WIREs Comp. Mol. Sci., 11(4), e1515, 2020.

  35. Lambros E., Lipparini F., Cisneros G.A., Paesani F. “A Many-Body, Fully Polarizable Approach to QM/MM Simulations”, J. Chem. Theo. Comp., 16, 7462-7472, 2020.

  36. Hix M.A., Wong L, Flath B., Chelico L., Cisneros G.A. “Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer”, NAR Cancer, 2, zcaa023, 2020.

  37. Hix M.A., Cisneros G.A. “Computational investigation of APOBEC3H substrate orientation and selectivity”, J. Phys. Chem. B, 124, 3903-3908, 2020.

  38. Vazquez-Montelongo E.A., Vazquez-Cervantes J.E., Cisneros G.A. “Current Status of AMOEBA–IL: A Multipolar/Polarizable Force Field for Ionic Liquids”, Int. J. Mol. Sci., 21(3), 697, 2020.

  39. Duke R.E., Cisneros G.A. “Ewald–Based Methods for Gaussian Integral Evaluation: Application to a New Parametrization of GEM*”, J. Mol. Model., 25:307, 2019.

  40. Das R., Vazquez-Montelongo E.A., Cisneros G.A., Wu J.I. “Ground State Destabilization in Uracil DNA Deglycosylase (UDG): Let’s Not Forget “Tautomeric Strain” in Substrates”, J. Am. Chem. Soc., 141, 13739-13743, 2019.

  41. Vazquez-Montelongo E.A., Cisneros G.A., Flores–Ruiz H.M. “Multipolar/Polarizable Molecular Dynamics Simulations of Liquid-Liquid Extraction of Benzene from Hydrocarbons Using Ionic Liquids”, J. Mol. Liq., 296, 111846, 2019.

  42. Koleva B.N., Gokcan H., Rizzo A.A., Lim R., Dit Fouque K.J., Choy A., Liriano M., Fernandez-Lima F., Korzhnev D., Cisneros G.A., Beuning P. “Dynamics of the E. coli beta clamp dimer interface and its influence on DNA loading”, Biophys. J., 117, 587-601, 2019.

  43. Leddin E.M., Cisneros G.A., “Comparison of DNA and RNA Substrate Effects on TET2 Structure”, in “Advances in Protein Chemistry and Structural Biology”, T. Karabencheva-Christova and C. Christov Eds., Elsevier, DOI: 10.1016/bs.apcsb.2019.05.002, 2019.

  44. Loco D., Lagardere L, Cisneros G.A., Scalmani G., Frisch M., Lipparini F., Mennucci B., Piquemal J.P., “Towards Large Scale Hybrid QM/MM Dynamics of Complex Systems with Advanced Point Dipole Polarizable Embeddings”, Chem. Sci., 10, 7200-7211, 2019.

  45. Walker A.R, Baddam N., Cisneros G.A., “Unfolding Pathways of Hen Egg White Lysozyme in Ethanol”, J. Phys. Chem. B, 123, 3267-3271, 2019.

  46. Gokcan H., Vazquez-Montelongo E.A., Cisneros G.A., “LICHEM 1.1: Recent Improvements and New Capabilities”, J. Chem. Theo. Comput., 15, 3056-3065, 2019.

  47. DeNizio J., Liu M., Leddin E.M., Cisneros G.A., Kohli R., “Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA”, Biochemistry, 58, 411-421, 2018.

  48. Vazquez-Montelongo E.A., Vazquez-Cervantes J.E., Cisneros G.A., “Polarizable ab initio QM/MM study of the reaction mechanism of N-tert-butyloxycarbonylation of aniline in [EMIm][BF4]”, Molecules, 23 (11), 2830, 2018.

  49. Torabifard H., Cisneros G.A., “Insight into Wild-Type and T1372E TET2-mediated 5hmC oxidation using ab initio QM/MM calculations” , Chem. Sci., 9, 8433-8445, 2018.

  50. Gahlon H.L., Walker A.R., Cisneros G.A., Lamers M.H., Rueda D., “Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant”, Phys. Chem. Chem. Phys., 20, 26892-26902, 2018.

  51. Silvestrov P., Maier S.J., Fang M., Cisneros G.A., “DNArCdb: A Database of Cancer Biomarkers in DNA Repair Genes that Includes Variants Related to Multiple Cancer Phenotypes”, DNA Rep., 70, 10-17, 2018.

  52. Antczak N.M., Walker A.R., Leddin E.M., Palad C., Swett R.J., Cisneros G.A., Beuning P.J., “Characterization of nine cancer-associated variants in human DNA polymerase kappa” , Chem. Res. Tox., 31, 697-711, 2018.

  53. Lohrman J., Vazquez-Montelongo E.A., Pramanik S., Day V.W., Hix M.A., Bowman-James K., Cisneros G.A., “Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses” , Inorg. Chem., 57, 9775-9778, 2018.

  54. Gokcan H., Kratz E.G., Darden T., Piquemal J.-P., Cisneros G.A., “QM/MM Simulations with the Gaussian Electrostatic Model, A Density-Based Polarizable Potential” , J. Phys. Chem. Lett., 9, 3062-3067, 2018.

  55. Silvestrov P., Cisneros G.A., “Insights on conformational changes in AlkD bound to DNA with a yatakemycin adduct from computational simulations” , Theo. Chem. Acc., 137, 78, 2018.

  56. Blanco-Diaz E.G., Vazquez-Montelongo E.A., Cisneros G.A., Castrejon-Gonzalez E.O., “Computational Investigation of Non-Covalent Interactions in 1-Butyl-3-Methylimidazolium/bis(Trifluoromethylsulfonyl)imide in EMD and NEMD” , J. Chem. Phys., 148, 054303, 2018.

  57. Tu Y.-J., Lin Z., Allen M.J., Cisneros G.A., “Molecular Dynamics Investigation of Solvent-Exchange Reactions on Lanthanide Ions in Water/1-Ethyl-3-Methylimidazolium Trifluoromethylsulfate ([EMIm][OTf])” , J. Chem. Phys., 148, 024503, 2018.

  58. Liyanage P.S., Walker A.R., Brenlla A., Cisneros G.A., Romano L.J., Rueda D., “Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations” , Sci. Reports, 7, 17383, 2017.

  59. Lagardere L., Jolly H.-L., Lipparini F., Aviat F., Stamm B., Jing Z.F., Harger M., Torabifard H., Cisneros G.A., Schnieders M.J., Gresh N., Maday Y., Ren P.Y., Ponder J.W., Piquemal J.-P., “Tinker-HP: a Massively Parallel Molecular Dynamics Package for Multiscale Simulations of Large Complex Systems with Advanced Polarizable Force Fields”, Chem. Sci., 9, 956-972, 2017.

  60. Torabifard H., Reed L., Berry M.T., Hein J.E., Menke E., Cisneros G.A., “Computational and Experimental Characterization of a Pyrrolidinium-Based Ionic Liquid for Electrolyte Applications “, J. Chem. Phys., 147, 161731, 2017.

  61. Walker A.R., Cisneros G.A., “Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants “, Chem. Res. Tox., 30, 1922-1935, 2017.

  62. Torabifard H., Cisneros G.A., “Computational Investigation of O2 Diffusion Through an Intra-molecular Tunnel in AlkB; Influence of Polarization on O2 Transport “, Chem. Sci., 8, 6230-6238, 2017.

  63. O’Brien J.S., Allen M.A., Cisneros G.A., “Computational Study of pH-Responsive Di-Lanthanide Complexes “, Int. J. Quantum Chem., 117, e25406, 2017.

  64. Walker A.R., Silvestrov P., Muller T.A., Podolski R.H., Dyson G., Hausinger R.P., Cisneros G.A., “ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding”, PLoS Comp. Bio., 13(2), e1005345, 2017.
  65. Walker A.R., Bonomi R., Popov V., Gelovani J.G., Cisneros G.A., “Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies “, J. Mol. Graph. Model., 71, 211-217, 2017.

  66. Liu M.Y., Torabifard H., Crawford D.J., DeNizio J.E., Cao X.-J., Garcia B.A., Cisneros G.A., Kohli R.M., “Mutations along a TET2 active site scaffold stall oxidation at 5-hydroxymethylcytosine “, Nature Chem. Bio., 13, 181-187, 2017.

  67. Gamage N-D.H., Stasny B., Kratz E.G., Stierstorfer J., Martin P.D., Cisneros G.A., Klapotke T.M., Winter C.H. “Energetic Materials Trends in 5- and 6-Membered Cyclic Peroxides Containing Hydroperoxy and Hydroxy Substituents”, Eur. J. Inorg. Chem., 31, 5036-5046, 2016.

  68. Tu Y-J., Allen M.J., Cisneros G.A, “Simulations of Water Exchange Dynamics on Lanthanide Ions in 1-Ethyl-3-Methylimidazolium Ethyl Sulfate ([EMIm][EtSO4]) and Water”, Phys. Chem. Chem. Phys., 18, 30323-30333, 2016.

  69. Zhao L., Udumbara M., Dewage S.W., Wood W.N., Veltri A.J., Cisneros G.A, Hendrickson T.L., “Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase “, FEBS Lett., 590, 3122-3132, 2016.

  70. Kratz E.G., Duke R.E., Cisneros G.A, “Long-Range Electrostatic Corrections in Multipolar/Polarizable QM/MM Simulations”, Theo. Chem. Acc., 135:166, 2016.

  71. Cisneros G.A, Wikfeldt K.T., Ojamae L., Lu J., Xu Y., Torabifard H., Bartok A.P., Csanyi G., Molinero V., Paesani F., “Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions”, Chem. Rev., 116, 7501-7528, 2016.

  72. Kratz E.G., Walker A.R., Lagardere L., Lipparini F., Piquemal J.P., Cisneros G.A, “LICHEM: A QM/MM program for simulations with multipolar-polarizable force fields”, J. Comp. Chem., 37, 1019-1029, 2016.

  73. Pratt A.C., Dewage S.W., Pang A., Biswas T., Barnard-Britson S., Cisneros, G.A., Tsodikov, O.V., “Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis”, J. Struct. Bio., 192, 76-87, 2015.

  74. Bonomi R.E., Mukhopadhyay U., Dewage S.W., Mahji A, Shavrin A, Najjar A., Yeh H.-H., Lu X, Magner T., Cisneros, G.A., Tong W.P., Alauddin M.M., Gelovani J.G., Turkman N., “Development of Novel Histone Deacetylase Class IIA-specific Substrate Radiotracers for PET imaging”, PLoS ONE, 10(8) e0133512, 2015.

  75. Torabifard H., Starovoytov O.N., Ren. P., Cisneros G.A., “Development of an AMOEBA water model using GEM distributed multipoles”, Theo. Chem. Acc., 134, 101:1-10, 2015.

  76. Fang D., Duke R.E., Cisneros G.A., “A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations”, J. Chem. Phys., 143, 044103, 2015.

  77. Bellow J., Yousif M., Fang D., Kratz E., Cisneros, G.A., Groysman S., “Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OtBu2Ph]”, Inorganic Chemistry, 54, 5624-5633, 2015.

  78. Dewage S.W., Cisneros G.A., “Computational Analysis of Ammonia Transfer along Two Intra-molecular Tunnels in Staphylococcus aureus Glutamine-dependent Amidotransferase (GatCAB)”, J. Phys. Chem. B, 119, 3669-3677, 2015.

  79. Pavel Silvestrov, Tina A. Muller, Kristen N. Clark, Robert P. Hausinger, Cisneros G.A., “Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)”, J. Mol. Graph., Model., 54, 123-130, 2014.

  80. Fang D., Cisneros G.A., “Alternative pathway for the reaction catalyzed by DNA dealkylase AlkB from ab initio QM/MM simulations”, J. Chem. Theo. Comp, 10, 5136-5148, 2014.

  81. Starovoytov O.N., Torabifard H., Cisneros G.A., “Development of AMOEBA Force Field for 1, 3-Dimethylimidazolium Based Ionic Liquids”, J. Phys. Chem. B, 118, 7156-7166, 2014.

  82. Chaudret R., Gresh N., Narth C., Lagardere L., Darden T., Cisneros G.A., Piquemal J.-P., “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”, J. Phys. Chem. A, 118, 7598-7612, 2014.

  83. Elias A., Cisneros G.A., “Computational Study of Putative Residues Involved in, DNA Synthesis Fidelity Checking in Thermus aquaticus DNA Polymerase I” , in Advances in Protein and Structural Biology: Biomolecular Modelling and Simulations, Vol. 96, Ed. T. Karabencheva-Christova, pp. 35–79, Elsevier, 2014.

  84. Piquemal J.-P., Cisneros G.A., “Status of the Gaussian Electrostatic Model, a Density Based Polarizable Force Field” , in Many-body effects and electrostatics in multi-scale computations of Biomolecules, Eds. Qiang Cui, Pengyu Ren and Markus Meuwly, pp. 269-300, Pan Stanford Publishing, 2014.

  85. Fang D., Piquemal J.-P., Liu S., Cisneros G.A., “DFT steric based energy decomposition analysis of intermolecular interactions”, Theo. Chem. Acc., 133, 1484:1-14, 2014.

  86. Duke R.E., Starovoytov O.N., Piquemal J.-P., Cisneros G.A., “GEM*: A Molecular Electronic Density–Based Force Field for Molecular Dynamics Simulations”, J. Chem. Theo. Comp., 10, 1361-1365, 2014.

  87. Cisneros G.A., Karttunen M., Ren P., Sagui C., “Classical Electrostatics for Biomolecular Simulations”, Chem. Rev., 114, 779-814, 2014.
  88. Bellow J.A., Fang D. Kovacevic N., Martin P.D., Shearer J., Cisneros G.A., Groysman S., “Novel Alkoxide Cluster Topologies Featuring Rare Seesaw Geometry at Transition Metals Centers”, Chem. Eur. J., 19, 12225-12228, 2013.

  89. Swett R.J., Elias A., Miller J.A., Dyson G.E., Cisneros G.A., “Hypothesis Driven Single Nucleotide Polymorphism Search (HyDn-SNP-S)”, DNA Repair, 12, 733-740, 2013.
  90. Burger S.K., Cisneros G.A., “Efficient Optimization of van der Waals Parameters based on Bulk Properties “, J. Comp. Chem., 34, 2313-2319, 2013.

  91. Swett R.J., Cisneros G.A., Feig A., “Disruption of intrinsic motions as a mechanism for enzyme inhibition”, Biophys J., 105, 494-501, 2013.

  92. Fang D., Lord R.L., Cisneros G.A., “QM/MM Calculations Show There is an Intersystem Crossing in the Hydrogen Abstraction Step in the Dealkylation Catalyzed by AlkB”, J. Phys. Chem. B, 117, 6410-6420, 2013.

  93. Fang D., Chaudret R., Piquemal J.P., Cisneros G.A., “Toward a Deeper understanding of Enzyme Reactions using the coupled ELF/NCI Analysis: Application to DNA repair enzymes”, J. Chem. Theo. Comp., 9, 2156-2160, 2013.

  94. Chaudret R., Gresh N., Cisneros G.A., Scemama A., Piquemal J.P., “Further refinements of next-generation force-fields: non empirical localization of off-centered-points in molecules”, Can. J. Chem., 99, 1-7, 2013.

  95. Cisneros G.A., Babin V., Sagui C., “Electrostatics Interactions in Classical Simulations”, in “Biomolecular Simulations: Methods and Protocols” for the Book Series: Methods in Molecular Biology, L. Monticelli and E. Salonen, Eds., Springer Science+Business Media New York, Vol. 924, pp. 243-270, DOI:10.1007/978-1-62703-017-5, 2013.

  96. Kraskkouskaya D., Drewry J.A., Doudo E., Burger S.K., Eaton J., Cisneros G.A., Gunning P.T., “Exploring the structural determinants of selective phosphopeptide recognition using bivalent metal–coordination complexes”, Chem. Med. Comm., 4, 289-292, 2013.

  97. Cisneros G.A., “Application of Gaussian Electrostatic Model (GEM) distributed multipoles in the AMOEBA force field”, J. Chem. Theo. Comp., 8, 5072-5080 2012.

  98. Moore J.D., Lord R.L. Cisneros G.A., Allen M.J., “Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe” , J. Am. Chem. Soc., 134, 17372-17375, 2012.

  99. Swett R., Cisneros G.A., Feig A., “Conformational Analysis of Clostridium difficile Toxin B and its Implications for Substrate Recognition”, PLoS ONE, 7 (7) , e41518, 2012.

  100. Pan W. Cisneros G.A., Hu H., Chaudret R., Hu X., Yang W., “Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways”, J. Phys. Chem. B., 116, 6889-6897, 2012.

  101. Graham S.E., Syeda FS. Cisneros G.A., “Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I”, Biochemistry, 51, 2569-2578, 2012.

  102. Zhao L., Dewage S.W., Bell M.J., Chang K.-M., Fatma S., Joshi N.V., Silva G.N., Cisneros G.A., Hendrickson T.L., “The kinase activity of the Helicobacter pylori Asp-tRNAAsn/Glu-tRNAGln amidotransferase is sensitive to distal mutations in its putative ammonia chanel”, Biochemistry, 51, 273, 285, 2012.
  103. Chaudret R., Piquemal J.P., Cisneros G.A., “Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations”, Phys. Chem. Chem. Phys, 13, 11239-11247, 2011.

  104. Chaudret R., Cisneros G.A., Parisel O. Piquemal J.P., “Unraveling Low Barrier Hydrogen Bonds in complex systems using a simple quantum topological criterion”, Chem. Eur. J., 17, 2833-2837, 2011.

  105. Cisneros G.A. “DFT study of a model system for the dealkylation step catalyzed by AlkB”, Interdiscip. Sci.: Comput. Life Sci., 2, 70-77, 2010.

  106. Elking D.M., Cisneros G.A., Piquemal J.P., Darden T.A., Pedersen L.G., “Gaussian Multipole Model (GMM)”, J. Chem. Theo. Comp., 6, 190-202, 2010.

  107. Cisneros G.A., Darden T.A., Gresh N., Reinhardt P., Parisel O., Pilme J., Piquemal J.-P., “Design of next generation polarizable force fields from ab initio computations: beyond point charges”, in “Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications” for the Book Series: Challenges and Advances in Computational Chemistry and Physics, D.M. York and T.-S. Lee, Eds, Springer-Verlag, ISBN: 978-1-4020-9955-7, pp. 137-172, 2009.

  108. Cisneros G.A., Yang W., “Comparison of reaction barriers in Energy and Free energy for enzyme catalysis”, in “Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications” for the Book Series: Challenges and Advances in Computational Chemistry and Physics, D.M. York and T.-S. Lee, Eds., Springer-Verlag, ISBN: 978-1-4020-9955-7, pp. 57-78, 2009.

  109. Chaudret R., Ulmer S., van Severen M.-C., Gresh, Parisel O., Cisneros G.A., Darden T.A., Piquemal J.-P., “Progress towards accurate molecular modeling of metal complexes using polarizable force fields”, AIP Conf. Proc., 1102 (1), 185-192, 2009.

  110. Cisneros G.A., Perera L., Schaaper R.M., Pedersen L.C., London R.E., Pedersen L.G., Darden T.A., “Reaction mechanism of the ɛ subunit of E. coli DNA polymerase III: Insights into active site metal coordination and catalytically significant residues”, J. Am. Chem. Soc., 131 (4), 1550-1556, 2009.

  111. Cisneros G.A., Perera L., Garcia-Diaz M., Bebenek K., Kunkel T.A., Pedersen L.G., “Catalytic mechanism of human DNA polymerase ʎ with Mg(II) and Mn(II) from ab initio quantum mechanics/molecular mechanics studies”, DNA Repair, 7, 1824-1834, 2008.

  112. Cisneros G.A., Tholander S.N-I, Parisel O., Darden T.A., Elking D., Perera L., Piquemal J.-P., “Simple formulas for improved point-charge electrostatics in clasical force fields and hybrid Quantum Mechanical/Molecular Mechanical embedding”, Int. J. Quantum Chem., 108 (11), 1905-1912,2008.

  113. Cisneros G.A., Elking, D., Piquemal J.-P., Darden T.A., “Numerical fitting of molecular properties to Hermite Gaussians”, J. Phys. Chem. A, 111, 12049-12056, 2007.

  114. Gresh N. Cisneros G.A., Darden T.A. Piquemal J.-P. “Anisotropic, polarizable molecular mechanics studies of inter-, intra-molecular interactions and ligand-macromolecule complexes. A bottom-up strategy”, J. Chem. Theo. Comp., 3, 1960-1986, 2007.

  115. Cisneros G.A., Piquemal J.-P. and Darden T.A. “Generalization of the Gaussian Electrostatic Model: extension to arbitrary angular momentum, distributed multipoles and speedup with reciprocal space methods”, J. Chem. Phys., 125, 184101, 2006.
    • Also selected to appear in: Virtual Journal of Biol. Phys. Res., 2006, vol. 12, issue 10.
  116. Piquemal J.-P., Perera L., Cisneros G.A., Ren P., Pedersen L.G., and Darden T.A., “Towards accurate solvation dynamics of divalent cations in water using the polarizable AMOEBA force field: from energetics to structure”, J. Chem. Phys., 125, 054511, 2006.

  117. Cisneros G.A., Piquemal J.-P., Darden T.A., “QM/MM electrostatic embedding with continuous and discrete functions”, J. Phys. Chem. B, 110, 13682-13684, 2006.

  118. Piquemal J-P, Cisneros G.A., Reinhardt P., Gresh N., Darden T.A., “Towards a force field based on density fitting”, J. Chem. Phys, 124, 104101, 2006.
    • Also selected to appear in: Virtual Journal of Biol. Phys. Res., 2006, vol. 11, issue 6.
  119. Cisneros G.A., Wang M., Silinski P., Fitzgerald M.C., Yang W., “Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase”, J. Phys. Chem. A, 110 (2), 700-708, 2006.

  120. Cisneros G.A., Piquemal J-P, Darden T.A., “Intermolecular electrostatic energies using density fitting’’, J. Chem. Phys., 123, 44109, 2005.
    • Also selected to appear in: Virtual Journal of Biol. Phys. Res., 2005, vol. 10, issue 4.
  121. Cisneros G.A., 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’’, J. Chem. Phys., 122, 114502, 2005.
    • Also selected to appear in: Virtual Journal of Biol. Phys. Res., 2005, vol. 9, issue 7.
  122. Liu H., Lu Z., Cisneros G.A., Yang W., “Parallel Iterative Reaction Path Optimization in Ab Initio Quantum Mechanical/Molecular Mechanical Modeling of Enzyme Reactions”, J. Chem. Phys., 121 (2), 697-706, 2004.
    • Also selected to appear in: Virtual Journal of Biol. Phys. Res., 2004, vol. 8, issue 1.
  123. Cisneros G.A., Wang M., Silinski P., Yang W., Fitzgerald M.C., “The Protein Backbone Makes Important Contributions to 4-Oxalocrotonate Tautomerase Enzyme Catalysis: Understanding from Experiment and Theory”, Biochemistry, 43 (22), 6885-6892, 2004.

  124. Goj L.A., Cisneros G.A., Yang W., Widenhoefer R., “Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization”, J. Organomet Chem, 687 (2), 489-507, 2003.
  125. Cisneros G.A., 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”, J. Am. Chem. Soc., 125 (34), 10348-10393, 2003.

  126. Perez-Marin L. Castro M., Otazo-Sanchez E., Cisneros G.A., “Density functional study of molecular recognition and reactivity of thiourea derivatives used in sensors for heavy metal polluting cations” Int. J. of Quantum Chem., 80 (4-5), 609-622, 2000.

  127. Ascencio-Gutierrez J.A., Perez-Marin L., Otazo-Sanchez E., Castro M., Contreras-Pulido D., Cisneros G.A., “Molecular and Quantum Mechanics Calculations for the 1-Furoyl-3-Phenylthiourea as a Pb2+ sensor”, Afinidad, 57 (487), 180-184 May-Jun, 2000.

  128. Cisneros G.A., Castro M., Salahub D.R., “DFT study of the structural and electronic properties of small Nin (n=2-4) clusters” Int. J. of Quantum Chem., 75 (4-5), 847-861, 1999.