Justin A. Lemkul (0000-0001-6661-8653)

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Biography

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.

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Virginia Tech: Blacksburg, VA, US

2023-06 to present | Associate Professor (Biochemistry)

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Justin A. Lemkul

https://orcid.org/0000-0001-6661-8653

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Biography

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Employment (4)

Virginia Tech: Blacksburg, VA, US

Virginia Polytechnic Institute and State University: Blacksburg, VA, US

University of Maryland Baltimore: Baltimore, MD, US

Virginia Polytechnic Institute and State University: Blacksburg, VA, US

Education and qualifications (2)

Virginia Polytechnic Institute and State University: Blacksburg, VA, US

Virginia Polytechnic Institute and State University: Blacksburg, VA, US

Professional activities (2)

Biophysical Society: Rockville, MD, US

American Chemical Society: Washington, DC, US

Funding (3)

Exploring the Role of Electronic Polarization in Biomolecular Folding and Interactions

Towards Computational Drug Design Against DNA G-Quadruplexes

Exploring RNA Folding and Dynamics Using a Polarizable Force Field

Research resources (1)

Studying Electronic Polarization in Biomolecular Dynamics and Small-Molecule Binding

Works (50 of 68)

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

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

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

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

Introductory Tutorials for Simulating Protein Dynamics with GROMACS

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TUPÃ: Electric field analyses for molecular simulations

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

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

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

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

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

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

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

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

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

Complete Genome Sequence of Fusobacterium necrophorum subsp. necrophorum ATCC 25286

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

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

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

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development

Polarizable force field for RNA based on the classical drude oscillator

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

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

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

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

Characterization of Mg2+ Distributions around RNA in Solution

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

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

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

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

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

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

Peer review (68 reviews for 12 publications/grants)