Justin Lemkul
Justin Lemkul
Assistant Professor at Virginia Tech
Verified email at vt.edu - Homepage
Title
Cited by
Cited by
Year
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
J Lee, X Cheng, JM Swails, MS Yeom, PK Eastman, JA Lemkul, S Wei, ...
Journal of chemical theory and computation 12 (1), 405-413, 2016
13862016
An empirical polarizable force field based on the classical drude oscillator model: development history and recent applications
JA Lemkul, J Huang, B Roux, AD MacKerell Jr
Chemical reviews 116 (9), 4983-5013, 2016
3532016
Assessing the stability of Alzheimer’s amyloid protofibrils using molecular dynamics
JA Lemkul, DR Bevan
The Journal of Physical Chemistry B 114 (4), 1652-1660, 2010
3512010
GridMAT‐MD: a grid‐based membrane analysis tool for use with molecular dynamics
WJ Allen, JA Lemkul, DR Bevan
Journal of computational chemistry 30 (12), 1952-1958, 2009
2582009
Practical considerations for building GROMOS-compatible small-molecule topologies
JA Lemkul, WJ Allen, DR Bevan
Journal of chemical information and modeling 50 (12), 2221-2235, 2010
1912010
Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations
JA Lemkul, DR Bevan
Biochemistry 49 (18), 3935-3946, 2010
1522010
Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions
IS Gutiérrez, FY Lin, K Vanommeslaeghe, JA Lemkul, KA Armacost, ...
Bioorganic & medicinal chemistry 24 (20), 4812-4825, 2016
1152016
The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease
JA Lemkul, DR Bevan
ACS Chemical Neuroscience 3 (11), 845-856, 2012
942012
Lipid composition influences the release of Alzheimer's amyloid β‐peptide from membranes
JA Lemkul, DR Bevan
Protein Science 20 (9), 1530-1545, 2011
942011
A comparative molecular dynamics analysis of the amyloid β-peptide in a lipid bilayer
JA Lemkul, DR Bevan
Archives of biochemistry and biophysics 470 (1), 54-63, 2008
762008
Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer’s amyloid β-peptide
SR Gerben, JA Lemkul, AM Brown, DR Bevan
Journal of Biomolecular Structure and Dynamics 32 (11), 1817-1832, 2014
742014
Perturbation of membranes by the amyloid β‐peptide–a molecular dynamics study
JA Lemkul, DR Bevan
The FEBS journal 276 (11), 3060-3075, 2009
742009
Implementation of extended L agrangian dynamics in GROMACS for polarizable simulations using the classical D rude oscillator model
JA Lemkul, B Roux, D van der Spoel, AD MacKerell Jr
Journal of computational chemistry 36 (19), 1473-1479, 2015
692015
Morin inhibits the early stages of amyloid β-peptide aggregation by altering tertiary and quaternary interactions to produce “off-pathway” structures
JA Lemkul, DR Bevan
Biochemistry 51 (30), 5990-6009, 2012
682012
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks
J Huang, JA Lemkul, PK Eastman, AD MacKerell Jr
Journal of computational chemistry 39 (21), 1682-1689, 2018
582018
Induced polarization influences the fundamental forces in DNA base flipping
JA Lemkul, A Savelyev, AD MacKerell Jr
The journal of physical chemistry letters 5 (12), 2077-2083, 2014
582014
Polarizable force field for DNA based on the classical drude oscillator: I. Refinement using quantum mechanical base stacking and conformational energetics
JA Lemkul, AD MacKerell Jr
Journal of chemical theory and computation 13 (5), 2053-2071, 2017
532017
Polarizable force field for DNA based on the classical Drude oscillator: II. Microsecond molecular dynamics simulations of duplex DNA
JA Lemkul, AD MacKerell Jr
Journal of chemical theory and computation 13 (5), 2072-2085, 2017
482017
Aggregation of Alzheimer’s amyloid β-peptide in biological membranes: A molecular dynamics study
JA Lemkul, DR Bevan
Biochemistry 52 (29), 4971-4980, 2013
452013
Polarizable force field for RNA based on the classical drude oscillator
JA Lemkul, AD MacKerell Jr
Journal of computational chemistry 39 (32), 2624-2646, 2018
442018
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Articles 1–20