Justin Lemkul

About

I am currently an Associate Professor in the Department of Biochemistry at Virginia Tech. My research focuses on applying atomistic molecular simulation methods to complex problems in biology and human health, with an emphasis on computer-aided drug design. My postdoctoral work was carried out at the University of Maryland, Baltimore, where I contributed to the development of the Drude polarizable force field for nucleic acids. This cutting-edge polarizable model drives much of our current research.

Work

Virginia Tech

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Associate Professor

US

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Virginia Polytechnic Institute and State University

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Assistant Professor

US

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University of Maryland Baltimore

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Postdoctoral Fellow

US

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Virginia Polytechnic Institute and State University

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Research Scientist

US

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Education

Virginia Polytechnic Institute and State University

United States of America
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Ph.D.

Virginia Polytechnic Institute and State University

United States of America
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B.S.

Publications

Weighted ensemble simulations with the Drude polarizable model

preprint

The pH-Dependent Specificity of Cathepsin S and Its Implications for Inflammatory Communications and Disease

Biochemistry

journal-article

Robustness in biomolecular simulations: Addressing challenges in data generation, analysis, and curation

Cell Reports Physical Science

journal-article

Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man

preprint

Robustness in Biomolecular Simulations: Addressing Challenges in Data Generation, Analysis, and Curation

preprint

Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations

Macromolecules

journal-article

Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1.0]

Living Journal of Computational Molecular Science

journal-article

Balancing Group 1 Monoatomic Ion–Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems

The Journal of Physical Chemistry B

journal-article

Introductory Tutorials for Simulating Protein Dynamics with GROMACS

The Journal of Physical Chemistry B

journal-article

Structural and electronic properties of polyethylene terephthalate (PET) from polarizable molecular dynamics simulations

preprint

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

The Journal of Physical Chemistry B

journal-article

Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications

Biochemistry

journal-article

Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β‐peptide

Proteins: Structure, Function, and Bioinformatics

journal-article

Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction

Biophysical Journal

journal-article

Quantifying Induced Dipole Effects in Small Molecule Permeation in a Model Phospholipid Bilayer

preprint

Dynamics, Electrostatics, and Thermodynamics of Base Pairing at theLTR-IIIQuadruplex:Duplex Junction

preprint

Structural dynamics of the methyl-coenzyme M reductase active site are influenced by coenzyme F430modifications

preprint

Pyroglutamylation Modulates Electronic Properties and the Conformational Ensemble of the Amyloid β -Peptide

preprint

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

Journal of Chemical Information and Modeling

journal-article

Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes

preprint

charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS

Journal of Chemical Information and Modeling

journal-article

Anin silicoapproach to determine inter-subunit affinities in human septin complexes

preprint

Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole–Dipole Interactions of the Amyloid β-Peptide

The Journal of Physical Chemistry B

journal-article

Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes

ACS Omega

journal-article

Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners

The Journal of Physical Chemistry B

journal-article

TUPÃ: Electric field analyses for molecular simulations

Journal of Computational Chemistry

journal-article

Effects of Familial Alzheimer’s Disease Mutations on the Folding Free Energy and Dipole-Dipole Interactions of the Amyloid β-Peptide

preprint

Integration of experimental data and use of automated fitting methods in developing protein force fields

Communications Chemistry

journal-article

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Journal of Computational Chemistry

journal-article

Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogenous Amyloid Oligomers

Journal of Computational Biophysics and Chemistry

journal-article

Cation competition and recruitment around the c-kit1 G-quadruplex using polarizable simulations

Biophysical Journal

journal-article

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

Journal of Chemical Information and Modeling

journal-article

Polarizable Molecular Dynamics Simulations of Two c-kit Oncogene Promoter G-Quadruplexes: Effect of Primary and Secondary Structure on Loop and Ion Sampling

Journal of Chemical Theory and Computation

journal-article

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

Nucleic Acids Research

journal-article

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

Nano Letters

journal-article

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

The Journal of Physical Chemistry B

journal-article

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

Living Journal of Computational Molecular Science

journal-article

Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286

Microbiology Resource Announcements

journal-article

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Journal of Physical Chemistry A

journal-article

Polarizable force field for RNA based on the classical drude oscillator

Journal of Computational Chemistry

journal-article

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

mSphere

journal-article

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

Journal of Computational Chemistry

journal-article

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

Biophysical Journal

journal-article

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

Journal of Molecular Biology

journal-article

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

Journal of Chemical Theory and Computation

journal-article

Structure and Dynamics of FosA-Mediated Fosfomycin Resistance in Klebsiella pneumoniae and Escherichia coli

Antimicrobial Agents and Chemotherapy

journal-article

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

Journal of Chemical Theory and Computation

journal-article

Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved Treatment of Protein-Ligand Interactions

Bioorganic & Medicinal Chemistry

journal-article

Characterization of Mg2+ Distributions around RNA in Solution

ACS Omega

journal-article

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

Journal of Physical Chemistry B

journal-article

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

Chemical Reviews

journal-article

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

PLoS ONE

journal-article

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

Journal of Physical Chemistry B

journal-article

CHARMM-GUI Input Generation for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations using the CHARMM Force Fields

Journal of Chemical Theory and Computation

journal-article

DIRECT-ID: An Automated Method to Identify and Quantify Conformational Variations - Application to β2-adrenergic GPCR

Journal of Computational Chemistry

journal-article

Implementation of Extended Lagrangian Dynamics in GROMACS for Polarizable Simulations Using the Classical Drude Oscillator Model

Journal of Computational Chemistry

journal-article

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

Journal of Physical Chemistry Letters

journal-article

Biophysical and Molecular-Dynamics Studies of Phosphatidic Acid Binding by the Dvl-2 DEP Domain

journal-article

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

journal-article

Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study

journal-article

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

journal-article

Aggregation of Alzheimer’s Amyloid β-Peptide in Biological Membranes: A Molecular Dynamics Study

Biochemistry

journal-article

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

journal-article

Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce “Off-Pathway” Structures

Biochemistry

journal-article

Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce “Off-Pathway” Structures

journal-article

Morin Inhibits the Early Stages of Amyloid β-Peptide Aggregation by Altering Tertiary and Quaternary Interactions to Produce ‘Off-Pathway’ Structures

Biochemistry

journal-article

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

journal-article

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

journal-article

Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations

journal-article

Practical Considerations for Building GROMOS-Compatible Small-Molecule Topologies

journal-article

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

Journal of Physical Chemistry B

journal-article

Assessing the Stability of Alzheimer’s Amyloid Protofibrils Using Molecular Dynamics

journal-article

Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations

Biochemistry

journal-article

Destabilizing Alzheimer’s Aβ 42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations

journal-article

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

journal-article

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

journal-article

A Comparative Molecular Dynamics Analysis of the Amyloid β-Peptide in a Lipid Bilayer

Archives of Biochemistry and Biophysics

journal-article

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

journal-article