List of works - Justin A Lemkul

A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer.

scientific article

Aggregation of Alzheimer's amyloid β-peptide in biological membranes: a molecular dynamics study

scientific article

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

scientific article (publication date: 11 May 2016)

Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics

scientific article published in February 2010

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

scientific article published on 19 October 2016

Biophysical and molecular-dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain

scientific article

Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane ⬇️

scientific article published on June 23, 2011

Characterization of Mg2+ Distributions around RNA in Solution.

scientific article published on 26 October 2016

Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide

scientific article

Complete Genome Sequence of Fusobacterium necrophorum subsp. ATCC 25286

scientific article published on 21 February 2019

DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

scientific article

From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]

scientific article published in 2019

FusoPortal: An interactive repository of hybrid MinION sequenced Fusobacterium genomes improves gene identification and characterization

article

FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization.

scientific article published on 5 July 2018

GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics

scientific article

HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions

article

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

scientific article published on 12 May 2015

Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides.

scientific article

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

scientific article

Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations

scientific article published on 18 May 2018

Ion Binding Properties and Dynamics of the <i>bcl-</i>2 G-Quadruplex Using a Polarizable Force Field

scientific article published on 02 December 2020

Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes.

scientific article

Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Cooperative Ion Binding

scientific article published on 20 December 2018

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

article

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions

scientific article published on 18 June 2016

Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study

scientific article

Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex

scientific article published on 8 May 2015

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

scientific article published on 11 April 2017

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

scientific article published on 11 April 2017

Polarizable force field for RNA based on the classical drude oscillator

scientific article published on 01 December 2018

Practical considerations for building GROMOS-compatible small-molecule topologies

scientific article published on 30 November 2010

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

scientific article published on 01 January 2020

Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

scientific article published on 06 December 2019

Simulations of monomeric amyloid β-peptide (1-40) with varying solution conditions and oxidation state of Met35: implications for aggregation

scientific article

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

article

Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli.

scientific article published on 5 September 2017

The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease ⬇️

scientific article published on August 27, 2012

Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

scientific article

List of works by Justin A Lemkul

A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer.

Aggregation of Alzheimer's amyloid β-peptide in biological membranes: a molecular dynamics study

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model

Biophysical and molecular-dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain

Characterization of Interactions between PilA from Pseudomonas aeruginosa Strain K and a Model Membrane ⬇️

Characterization of Mg2+ Distributions around RNA in Solution.

Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide

Complete Genome Sequence of Fusobacterium necrophorum subsp. ATCC 25286

DIRECT-ID: An automated method to identify and quantify conformational variations--application to β2 -adrenergic GPCR.

From Proteins to Perturbed Hamiltonians: A Suite of Tutorials for the GROMACS-2018 Molecular Simulation Package [Article v1.0]

FusoPortal: An interactive repository of hybrid MinION sequenced Fusobacterium genomes improves gene identification and characterization

FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization.

GridMAT-MD: a grid-based membrane analysis tool for use with molecular dynamics

HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides.

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations

Ion Binding Properties and Dynamics of the <i>bcl-</i>2 G-Quadruplex Using a Polarizable Force Field

Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes.

Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Cooperative Ion Binding

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions

Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study

Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

Polarizable force field for RNA based on the classical drude oscillator

Practical considerations for building GROMOS-compatible small-molecule topologies

Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes

Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

Simulations of monomeric amyloid β-peptide (1-40) with varying solution conditions and oxidation state of Met35: implications for aggregation

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli.

The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease ⬇️

Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations