| Year |
Citation |
Score |
| 2024 |
Maghsoud Y, Roy A, Leddin EM, Cisneros GA. Effects of the Y432S Cancer-Associated Variant on the Reaction Mechanism of Human DNA Polymerase κ. Journal of Chemical Information and Modeling. PMID 38717969 DOI: 10.1021/acs.jcim.4c00339 |
0.814 |
|
| 2024 |
Nochebuena J, Liu S, Cisneros GA. Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations. The Journal of Chemical Physics. 160. PMID 38557841 DOI: 10.1063/5.0203020 |
0.505 |
|
| 2023 |
Nochebuena J, Piquemal JP, Liu S, Cisneros GA. Cooperativity and Frustration Effects (or Lack Thereof) in Polarizable and Non-polarizable Force Fields. Journal of Chemical Theory and Computation. 19: 7715-7730. PMID 37888874 DOI: 10.1021/acs.jctc.3c00762 |
0.623 |
|
| 2023 |
Case DA, Aktulga HM, Belfon K, Cerutti DS, Cisneros GA, Cruzeiro VWD, Forouzesh N, Giese TJ, Götz AW, Gohlke H, Izadi S, Kasavajhala K, Kaymak MC, King E, Kurtzman T, et al. AmberTools. Journal of Chemical Information and Modeling. 63: 6183-6191. PMID 37805934 DOI: 10.1021/acs.jcim.3c01153 |
0.481 |
|
| 2022 |
Simonin-Wilmer I, Ossio R, Leddin EM, Harland M, Pooley KA, Martil de la Garza MG, Obolenski S, Hewinson J, Wong CC, Iyer V, Taylor JC, Newton-Bishop JA, Bishop DT, Cisneros GA, Iles MM, et al. Population-based analysis of variants in a cutaneous melanoma case-control cohort. Journal of Medical Genetics. PMID 36539277 DOI: 10.1136/jmg-2022-108776 |
0.767 |
|
| 2022 |
Yeaton A, Cayanan G, Loghavi S, Dolgalev I, Leddin EM, Loo CE, Torabifard H, Nicolet D, Wang J, Corrigan K, Paraskevopoulou V, Starczynowski DT, Wang E, Abdel-Wahab O, Viny AD, ... ... Cisneros GA, et al. The impact of inflammation-induced tumor plasticity during myeloid transformation. Cancer Discovery. PMID 35924979 DOI: 10.1158/2159-8290.CD-21-1146 |
0.747 |
|
| 2022 |
Ravishankar K, Jiang X, Leddin EM, Morcos F, Cisneros GA. Computational compensatory mutation discovery approach: Predicting a PARP1 variant rescue mutation. Biophysical Journal. PMID 35642254 DOI: 10.1016/j.bpj.2022.05.036 |
0.787 |
|
| 2022 |
Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. Journal of Chemical Theory and Computation. PMID 35575306 DOI: 10.1021/acs.jctc.2c00029 |
0.795 |
|
| 2022 |
Li AWH, Zabrady K, Bainbridge LJ, Zabrady M, Naseem-Khan S, Berger MB, Kolesar P, Cisneros GA, Doherty AJ. Molecular basis for the initiation of DNA primer synthesis. Nature. PMID 35508653 DOI: 10.1038/s41586-022-04695-0 |
0.798 |
|
| 2022 |
Naseem-Khan S, Berger MB, Leddin EM, Maghsoud Y, Cisneros GA. Impact of Remdesivir Incorporation along the Primer Strand on SARS-CoV-2 RNA-Dependent RNA Polymerase. Journal of Chemical Information and Modeling. PMID 35435671 DOI: 10.1021/acs.jcim.2c00201 |
0.767 |
|
| 2021 |
Naseem-Khan S, Piquemal JP, Cisneros GA. Improvement of the Gaussian Electrostatic Model by separate fitting of Coulomb and exchange-repulsion densities and implementation of a new dispersion term. The Journal of Chemical Physics. 155: 194103. PMID 34800949 DOI: 10.1063/5.0072380 |
0.794 |
|
| 2021 |
Berger MB, Walker AR, Vázquez-Montelongo EA, Cisneros GA. Computational investigations of selected enzymes from two iron and α-ketoglutarate-dependent families. Physical Chemistry Chemical Physics : Pccp. 23: 22227-22240. PMID 34586107 DOI: 10.1039/d1cp03800a |
0.723 |
|
| 2021 |
Nochebuena J, Naseem-Khan S, Cisneros GA. Development and application of quantum mechanics/molecular mechanics methods with advanced polarizable potentials. Wiley Interdisciplinary Reviews. Computational Molecular Science. 11. PMID 34367343 DOI: 10.1002/wcms.1515 |
0.796 |
|
| 2021 |
Hix MA, Leddin EM, Cisneros GA. Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations. Journal of Chemical Theory and Computation. 17: 4524-4537. PMID 34087064 DOI: 10.1021/acs.jctc.1c00313 |
0.81 |
|
| 2020 |
Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids. International Journal of Molecular Sciences. 21: 697. PMID 31973103 DOI: 10.3390/Ijms21030697 |
0.305 |
|
| 2019 |
Loco D, Lagardère L, Cisneros GA, Scalmani G, Frisch M, Lipparini F, Mennucci B, Piquemal JP. Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings. Chemical Science. 10: 7200-7211. PMID 31588288 DOI: 10.1039/C9Sc01745C |
0.538 |
|
| 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 |
0.803 |
|
| 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 |
0.39 |
|
| 2019 |
Das R, Vázquez-Montelongo EA, Cisneros GA, Wu JI. Ground State Destabilization in Uracil DNA Glycosylase (UDG): Let's Not Forget "Tautomeric Strain" in Substrates. Journal of the American Chemical Society. PMID 31434485 DOI: 10.1021/Jacs.9B06447 |
0.375 |
|
| 2019 |
Koleva BN, Gokcan H, Rizzo AA, Lim S, Jeanne Dit Fouque K, Choy A, Liriano ML, Fernandez-Lima F, Korzhnev DM, Cisneros GA, Beuning PJ. Dynamics of the E. coli β-Clamp Dimer Interface and Its Influence on DNA Loading. Biophysical Journal. PMID 31349986 DOI: 10.1016/J.Bpj.2019.06.035 |
0.791 |
|
| 2019 |
Walker AR, Baddam N, Cisneros GA. Unfolding Pathways of Hen Egg White Lysozyme in Ethanol. The Journal of Physical Chemistry. B. PMID 30912946 DOI: 10.1021/Acs.Jpcb.9B01694 |
0.723 |
|
| 2019 |
Gokcan H, Vazquez Montelongo EA, Cisneros GA. LICHEM 1.1: Recent Improvements and New Capabilities. Journal of Chemical Theory and Computation. PMID 30908049 DOI: 10.1021/Acs.Jctc.9B00028 |
0.784 |
|
| 2019 |
Vázquez-Montelongo EA, Cisneros GA, Flores-Ruiz HM. Multipolar/polarizable molecular dynamics simulations of Liquid–Liquid extraction of benzene from hydrocarbons using ionic liquids Journal of Molecular Liquids. 296: 111846. DOI: 10.1016/J.Molliq.2019.111846 |
0.334 |
|
| 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 |
0.768 |
|
| 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 |
0.79 |
|
| 2018 |
Vázquez-Montelongo EA, Vázquez-Cervantes JE, Cisneros GA. Polarizable ab initio QM/MM Study of the Reaction Mechanism of N-tert-Butyloxycarbonylation of Aniline in [EMIm][BF4] Molecules. 23: 2830. PMID 30384470 DOI: 10.3390/Molecules23112830 |
0.365 |
|
| 2018 |
Gahlon HL, Walker AR, Cisneros GA, Lamers MH, Rueda DS. Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant. Physical Chemistry Chemical Physics : Pccp. PMID 30345999 DOI: 10.1039/C8Cp04112A |
0.744 |
|
| 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 |
0.744 |
|
| 2018 |
Lohrman J, Vázquez-Montelongo EA, Pramanik S, Day VW, Hix MA, Bowman-James K, Cisneros GA. Characterizing Hydrogen-Bond Interactions in Pyrazinetetracarboxamide Complexes: Insights from Experimental and Quantum Topological Analyses. Inorganic Chemistry. PMID 30088923 DOI: 10.1021/Acs.Inorgchem.8B00627 |
0.317 |
|
| 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. PMID 30078993 |
0.758 |
|
| 2018 |
Antczak NM, Walker AR, Stern HR, Leddin EM, Palad C, Coulther TA, Swett RJ, Cisneros GA, Beuning PJ. Characterization of nine cancer-associated variants in human DNA polymerase κ. Chemical Research in Toxicology. PMID 30004685 DOI: 10.1021/Acs.Chemrestox.8B00055 |
0.774 |
|
| 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 |
0.788 |
|
| 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 |
0.797 |
|
| 2018 |
Blanco-Díaz EG, Vázquez-Montelongo EA, Cisneros GA, Castrejón-González EO. Computational investigation of non-covalent interactions in 1-butyl 3-methylimidazolium/bis(trifluoromethylsulfonyl)imide [bmim][TfN] in EMD and NEMD. The Journal of Chemical Physics. 148: 054303. PMID 29421909 DOI: 10.1063/1.5017987 |
0.343 |
|
| 2018 |
Tu YJ, Lin Z, Allen MJ, Cisneros GA. Molecular dynamics investigation of water-exchange reactions on lanthanide ions in water/1-ethyl-3-methylimidazolium trifluoromethylsufate ([EMIm][OTf]). The Journal of Chemical Physics. 148: 024503. PMID 29331119 DOI: 10.1063/1.4997008 |
0.742 |
|
| 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 |
0.771 |
|
| 2017 |
Liyanage PS, Walker AR, Brenlla A, Cisneros GA, Romano LJ, Rueda D. Bulky Lesion Bypass Requires Dpo4 Binding in Distinct Conformations. Scientific Reports. 7: 17383. PMID 29234107 DOI: 10.1038/S41598-017-17643-0 |
0.744 |
|
| 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 |
0.759 |
|
| 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 |
0.762 |
|
| 2017 |
Walker AR, Cisneros GA. Computational Simulations of DNA Polymerases: Detailed Insights on Structure/Function/Mechanism from Native Proteins to Cancer Variants. Chemical Research in Toxicology. PMID 28877429 DOI: 10.1021/Acs.Chemrestox.7B00161 |
0.753 |
|
| 2017 |
Walker AR, Silvestrov P, Müller TA, Podolsky RH, Dyson G, Hausinger RP, Cisneros GA. ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding. Plos Computational Biology. 13: e1005345. PMID 28231280 DOI: 10.1371/Journal.Pcbi.1005345 |
0.774 |
|
| 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 |
0.79 |
|
| 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 |
0.755 |
|
| 2016 |
Tu YJ, Allen MJ, Cisneros GA. Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water. Physical Chemistry Chemical Physics : Pccp. 18: 30323-30333. PMID 27828553 DOI: 10.1039/C6Cp04957E |
0.745 |
|
| 2016 |
Tu YJ, Allen MJ, Cisneros GA. Correction: Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water. Physical Chemistry Chemical Physics : Pccp. PMID 27711761 DOI: 10.1039/c6cp90231f |
0.728 |
|
| 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 |
0.778 |
|
| 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 |
0.744 |
|
| 2016 |
Gamage NH, Stiasny B, Kratz EG, Stierstorfer J, Martin PD, Cisneros GA, Klapötke TM, Winter CH. Energetic Materials Trends in 5- and 6-Membered Cyclic Peroxides Containing Hydroperoxy and Hydroxy Substituents European Journal of Inorganic Chemistry. 2016: 5036-5043. DOI: 10.1002/Ejic.201600767 |
0.759 |
|
| 2015 |
Pratt AC, Dewage SW, Pang AH, Biswas T, Barnard-Britson S, Cisneros GA, Tsodikov OV. Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis. Journal of Structural Biology. 192: 76-87. PMID 26296329 DOI: 10.1016/J.Jsb.2015.08.010 |
0.796 |
|
| 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 |
0.752 |
|
| 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 |
0.533 |
|
| 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 |
0.753 |
|
| 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 |
0.784 |
|
| 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 |
0.755 |
|
| 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 |
0.581 |
|
| 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 |
0.761 |
|
| 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 |
0.377 |
|
| 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 |
0.509 |
|
| 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 |
0.768 |
|
| 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 |
0.797 |
|
| 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 |
0.608 |
|
| 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 |
0.499 |
|
| 2014 |
Cisneros GA, Karttunen M, Ren P, Sagui C. Correction to Classical Electrostatics for Biomolecular Simulations Chemical Reviews. 114: 5116-5116. DOI: 10.1021/Cr500124K |
0.651 |
|
| 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 |
0.76 |
|
| 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 |
0.707 |
|
| 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 |
0.796 |
|
| 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 |
0.424 |
|
| 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 |
0.784 |
|
| 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 |
0.784 |
|
| 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 |
0.486 |
|
| 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 |
0.596 |
|
| 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 |
0.76 |
|
| 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 |
0.766 |
|
| 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 |
0.779 |
|
| 2013 |
Zhao L, Dewage SW, Bell MJ, Chang K, Fatma S, Joshi N, Silva G, Cisneros GA, Hendrickson TL. Correction to The Kinase Activity of the Helicobacter pyloriAsp-tRNAAsn/Glu-tRNAGln Amidotransferase Is Sensitive to Distal Mutations in Its Putative Ammonia Tunnel Biochemistry. 52: 2381-2381. DOI: 10.1021/Bi400291U |
0.761 |
|
| 2012 |
Cisneros GA. Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field. Journal of Chemical Theory and Computation. 8: 5072-80. PMID 26593198 DOI: 10.1021/Ct300630U |
0.337 |
|
| 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 |
0.787 |
|
| 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 |
0.795 |
|
| 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 |
0.38 |
|
| 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 |
0.777 |
|
| 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 |
0.775 |
|
| 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 |
0.776 |
|
| 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 |
0.368 |
|
| 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 |
0.75 |
|
| 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 |
0.765 |
|
| 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 |
0.745 |
|
| 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 |
0.69 |
|
| 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 |
0.712 |
|
| 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 |
0.699 |
|
| 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 |
0.717 |
|
| 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 |
0.792 |
|
| 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 |
0.697 |
|
| 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 |
0.681 |
|
| 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 |
0.63 |
|
| 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 |
0.697 |
|
| 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 |
0.673 |
|
| 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 |
0.683 |
|
| 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 |
0.653 |
|
| 2004 |
Goj LA, Cisneros GA, Yang W, Widenhoefer RA. Erratum to “Dramatic effect of homoallylic substitution on the rate of palladium-catalyzed diene cycloisomerization” [J. Organomet. Chem. 687 (2003) 498–507] Journal of Organometallic Chemistry. 689: 2845. DOI: 10.1016/J.Jorganchem.2004.06.001 |
0.566 |
|
| 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 |
0.732 |
|
| 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 |
0.584 |
|
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