Lista de obras - Gerardo Andrés Cisneros

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

artículo científico publicado en 2020

A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations

artículo científico publicado en 2015

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding

artículo científico publicado en 2017

Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB.

artículo científico publicado en 2013

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

artículo científico publicado en 2003

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

artículo científico publicado en 2014

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

artículo científico publicado en 2007

Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field

artículo científico publicado en 2012

Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways

artículo científico publicado en 2012

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

artículo científico publicado en 2008

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

scientific article published on 30 July 2018

Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase.

artículo científico publicado en 2016

Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations

scientific article published on 04 June 2021

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

artículo científico publicado en 2017

Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).

artículo científico publicado en 2015

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

artículo científico publicado en 2017

Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.

artículo científico publicado en 2012

Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I.

artículo científico publicado en 2014

Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe.

artículo científico publicado en 2012

Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition

artículo científico publicado en 2012

Correction: Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

artículo científico publicado en 2016

Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations.

artículo científico publicado en 2011

Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids

scientific article published on 21 January 2020

DFT study of a model system for the dealkylation step catalyzed by AlkB.

artículo científico publicado en 2010

DFT-steric-based energy decomposition analysis of intermolecular interactions

article

Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids

artículo científico publicado en 2014

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations

artículo científico publicado en 2022

Efficient optimization of van der Waals parameters from bulk properties

artículo científico publicado en 2013

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of <i>Blastochloris viridis</i>’ Light Harvesting 1-Reaction Center Complex

artículo científico publicado en 2022

Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM

scientific article published on 09 September 2019

GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations

artículo científico publicado en 2014

Gaussian Multipole Model (GMM)

artículo científico publicado en 2010

Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

artículo científico publicado en 2006

Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)

artículo científico publicado en 2014

Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S).

artículo científico publicado en 2013

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

scientific article published on 11 September 2018

Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies

artículo científico publicado en 2016

LICHEM 1.1: Recent Improvements and New Capabilities

scientific article published on 02 April 2019

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

scientific article published on 17 June 2016

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

artículo científico publicado en 2016

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

artículo científico publicado en 2016

Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain

artículo científico publicado en 2015

Novel alkoxide cluster topologies featuring rare seesaw geometry at transition metal centers

scientific article published on 09 August 2013

Numerical fitting of molecular properties to Hermite Gaussians

artículo científico publicado en 2007

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions

artículo científico publicado en 2004

Polarizable QM/MM Study of the Reaction Mechanism of --Butyloxycarbonylation of Aniline in [EMIm][BF₄]

artículo científico publicado en 2018

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

artículo científico publicado en 2018

Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions

artículo científico publicado en 2006

Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

scientific article published on February 2009

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods

artículo científico publicado en 2005

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.

artículo científico publicado en 2014

Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA

artículo científico publicado en 2018

Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

artículo científico publicado en 2008

Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

artículo científico publicado en 2016

Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer

artículo científico publicado en 2020

Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis

artículo científico publicado en 2015

Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OC(t)Bu2Ph].

artículo científico publicado en 2015

The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel

artículo científico publicado en 2011

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

artículo científico publicado en 2004

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase

artículo científico publicado en 2006

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

artículo científico publicado en 2017

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

artículo científico publicado en 2013

Towards a force field based on density fitting

artículo científico publicado en 2006

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

scientific article published on 01 August 2006

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

scientific article published on 11 June 2019

Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol

artículo científico publicado en 2019

Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion

artículo científico publicado en 2011

Lista de obras de Gerardo Andrés Cisneros

A Many-Body, Fully Polarizable Approach to QM/MM Simulations

A new smoothing function to introduce long-range electrostatic effects in QM/MM calculations

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding

Ab initio QM/MM calculations show an intersystem crossing in the hydrogen abstraction step in dealkylation catalyzed by AlkB.

Ab initio QM/MM study shows there is no general acid in the reaction catalyzed by 4-oxalocrotonate tautomerase

Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand-Macromolecule Complexes. A Bottom-Up Strategy

Application of Gaussian Electrostatic Model (GEM) Distributed Multipoles in the AMOEBA Force Field

Catalytic mechanism of 4-oxalocrotonate tautomerase: significances of protein-protein interactions on proton transfer pathways

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

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

Characterization of tunnel mutants reveals a catalytic step in ammonia delivery by an aminoacyl-tRNA amidotransferase.

Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations

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

Computational analysis of ammonia transfer along two intramolecular tunnels in Staphylococcus aureus glutamine-dependent amidotransferase (GatCAB).

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

Computational prediction of residues involved in fidelity checking for DNA synthesis in DNA polymerase I.

Computational study of putative residues involved in DNA synthesis fidelity checking in Thermus aquaticus DNA polymerase I.

Concentration-independent pH detection with a luminescent dimetallic Eu(III)-based probe.

Conformational analysis of Clostridium difficile toxin B and its implications for substrate recognition

Correction: Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations.

Current Status of AMOEBA-IL: A Multipolar/Polarizable Force Field for Ionic Liquids

DFT study of a model system for the dealkylation step catalyzed by AlkB.

DFT-steric-based energy decomposition analysis of intermolecular interactions

Development of AMOEBA force field for 1,3-dimethylimidazolium based ionic liquids

Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations

Efficient optimization of van der Waals parameters from bulk properties

Electronic Structure Effects Related to the Origin of the Remarkable Near-Infrared Absorption of <i>Blastochloris viridis</i>’ Light Harvesting 1-Reaction Center Complex

Ewald-based methods for Gaussian integral evaluation: application to a new parameterization of GEM

GEM*: A Molecular Electronic Density-Based Force Field for Molecular Dynamics Simulations

Gaussian Multipole Model (GMM)

Generalization of the Gaussian electrostatic model: extension to arbitrary angular momentum, distributed multipoles, and speedup with reciprocal space methods

Homology modeling, molecular dynamics, and site-directed mutagenesis study of AlkB human homolog 1 (ALKBH1)

Hypothesis driven single nucleotide polymorphism search (HyDn-SNP-S).

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

Investigating carbohydrate based ligands for galectin-3 with docking and molecular dynamics studies

LICHEM 1.1: Recent Improvements and New Capabilities

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

Modeling Molecular Interactions in Water: From Pairwise to Many-Body Potential Energy Functions.

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

Novel Histone Deacetylase Class IIa Selective Substrate Radiotracers for PET Imaging of Epigenetic Regulation in the Brain

Novel alkoxide cluster topologies featuring rare seesaw geometry at transition metal centers

Numerical fitting of molecular properties to Hermite Gaussians

Parallel iterative reaction path optimization in ab initio quantum mechanical/molecular mechanical modeling of enzyme reactions

Polarizable QM/MM Study of the Reaction Mechanism of --Butyloxycarbonylation of Aniline in [EMIm][BF₄]

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

Quantum mechanics/molecular mechanics electrostatic embedding with continuous and discrete functions

Reaction mechanism of the epsilon subunit of E. coli DNA polymerase III: insights into active site metal coordination and catalytically significant residues.

Reaction path determination for quantum mechanical/molecular mechanical modeling of enzyme reactions by combining first order and second order "chain-of-replicas" methods

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.

Selectivity and Promiscuity in TET-mediated oxidation of 5-methylcytosine in DNA and RNA

Simple Formulas for Improved Point-Charge Electrostatics in Classical Force Fields and Hybrid Quantum Mechanical/Molecular Mechanical Embedding.

Simulations of the water exchange dynamics of lanthanide ions in 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) and water

Single-nucleotide polymorphism of the DNA cytosine deaminase APOBEC3H haplotype I leads to enzyme destabilization and correlates with lung cancer

Structural and computational dissection of the catalytic mechanism of the inorganic pyrophosphatase from Mycobacterium tuberculosis

Synthesis and Reactions of 3d Metal Complexes with the Bulky Alkoxide Ligand [OC(t)Bu2Ph].

The kinase activity of the Helicobacter pylori Asp-tRNA(Asn)/Glu-tRNA(Gln) amidotransferase is sensitive to distal mutations in its putative ammonia tunnel

The protein backbone makes important contributions to 4-oxalocrotonate tautomerase enzyme catalysis: understanding from theory and experiment

Theoretical and experimental determination on two substrates turned over by 4-oxalocrotonate tautomerase

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

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

Towards a force field based on density fitting

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Towards large scale hybrid QM/MM dynamics of complex systems with advanced point dipole polarizable embeddings

Unfolding Pathways of Hen Egg-White Lysozyme in Ethanol

Unraveling low-barrier hydrogen bonds in complex systems with a simple quantum topological criterion