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List of works by Gerardo Andrés Cisneros

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

scientific article published on 19 November 2020

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

scientific article published in July 2015

ALKBH7 Variant Related to Prostate Cancer Exhibits Altered Substrate Binding

scientific article

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

scientific article published on 16 May 2013

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

scientific article published in August 2003

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

scientific article

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

scientific article

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

scientific article published on 06 September 2012

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

scientific article published on 28 March 2012

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

scientific article published on 30 August 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.

scientific article published on 8 August 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

scientific article

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

scientific article published on 20 February 2015

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

scientific article published on 5 July 2017

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

scientific article published on 15 March 2012

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

scientific article

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

scientific article

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

scientific article (publication date: 2012)

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

scientific article published on 14 September 2016

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

scientific article

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.

scientific article published on 28 January 2010

DFT-steric-based energy decomposition analysis of intermolecular interactions

article

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

scientific article published on 17 June 2014

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

scientific article published on 16 May 2022

Efficient optimization of van der Waals parameters from bulk properties

scientific article published on 5 July 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

scientific article published on 29 June 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

scientific article published on 3 March 2014

Gaussian Multipole Model (GMM)

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

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.

scientific article published on 17 May 2016

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

scientific article

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

scientific article published on 5 August 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

scientific article published on November 2007

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

scientific article published in July 2004

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

scientific article published on 31 October 2018

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

scientific article published on 23 May 2018

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

scientific article published on July 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

scientific article published in March 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.

scientific article published on 19 June 2014

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

scientific article published on 14 November 2018

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

scientific article published on January 2008

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

scientific article

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

scientific article published on 17 September 2020

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

scientific article

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

scientific article published on 4 June 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

scientific article published on 29 December 2011

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

scientific article

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

scientific article published in January 2006

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

scientific article

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

scientific article published on 26 April 2013

Towards a force field based on density fitting

scientific article

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

scientific article published on 04 April 2019

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

scientific article published on 09 February 2011

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