Justin Alan Lemkul - Publications

Virginia Polytechnic and State University, United States 
Biochemistry, computational chemistry

33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Lemkul JA, MacKerell AD. Polarizable force field for RNA based on the classical drude oscillator. Journal of Computational Chemistry. 39: 2624-2646. PMID 30515902 DOI: 10.1002/jcc.25709  1
2018 van der Spoel D, Ghahremanpour MM, Lemkul JA. Small Molecule Thermochemistry: A Tool For Empirical Force Field Development. The Journal of Physical Chemistry. A. PMID 30362355 DOI: 10.1021/acs.jpca.8b09867  0.44
2018 Hollingsworth LR, Lemkul JA, Bevan DR, Brown AM. HIV-1 Env gp41 Transmembrane Domain Dynamics Are Modulated by Lipid, Water, and Ion Interactions. Biophysical Journal. 115: 84-94. PMID 29972814 DOI: 10.1016/j.bpj.2018.05.022  1
2018 Davidson DS, Brown AM, Lemkul JA. Insights into Stabilizing Forces in Amyloid Fibrils of Differing Sizes from Polarizable Molecular Dynamics Simulations. Journal of Molecular Biology. PMID 29782833 DOI: 10.1016/j.jmb.2018.05.020  0.84
2018 Huang J, Lemkul JA, Eastman PK, MacKerell AD. Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. Journal of Computational Chemistry. PMID 29727037 DOI: 10.1002/jcc.25339  1
2017 Klontz EH, Tomich AD, Günther S, Lemkul JA, Deredge D, Silverstein Z, Shaw JF, McElheny C, Doi Y, Wintrode P, MacKerell AD, Sluis-Cremer N, Sundberg EJ. Structure and dynamics of FosA-mediated fosfomycin resistance in Klebsiella pneumoniae and Escherichia coli. Antimicrobial Agents and Chemotherapy. PMID 28874374 DOI: 10.1128/AAC.01572-17  1
2017 Lemkul JA, MacKerell AD. 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. 13: 2053-2071. PMID 28399366 DOI: 10.1021/acs.jctc.7b00067  1
2017 Lemkul JA, MacKerell AD. 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. PMID 28398748 DOI: 10.1021/acs.jctc.7b00068  1
2016 Lemkul JA, Lakkaraju SK, MacKerell AD. Characterization of Mg(2+) Distributions around RNA in Solution. Acs Omega. 1: 680-688. PMID 27819065 DOI: 10.1021/acsomega.6b00241  1
2016 Lemkul JA, MacKerell AD. Balancing the Interactions of Mg(2+) in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model. The Journal of Physical Chemistry. B. 120: 11436-11448. PMID 27759379 DOI: 10.1021/acs.jpcb.6b09262  1
2016 Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL, MacKerell AD. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. Bioorganic & Medicinal Chemistry. PMID 27353885 DOI: 10.1016/j.bmc.2016.06.034  0.84
2016 Lemkul JA, Huang J, Roux B, MacKerell AD. An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications. Chemical Reviews. PMID 26815602 DOI: 10.1021/acs.chemrev.5b00505  0.84
2015 Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/acs.jctc.5b00935  0.84
2015 Lemkul JA, Huang J, MacKerell AD. Induced Dipole-Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides. The Journal of Physical Chemistry. B. PMID 26629591 DOI: 10.1021/acs.jpcb.5b09978  0.84
2015 Lakkaraju SK, Lemkul JA, Huang J, MacKerell AD. DIRECT-ID: An automated method to identify and quantify conformational variations-application to β2 -adrenergic GPCR. Journal of Computational Chemistry. PMID 26558323 DOI: 10.1002/jcc.24231  0.84
2015 Lemkul JA, Roux B, van der Spoel D, MacKerell AD. Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. Journal of Computational Chemistry. 36: 1473-9. PMID 25962472 DOI: 10.1002/jcc.23937  0.84
2015 Lemkul JA, Lewis SN, Bassaganya-Riera J, Bevan DR. Phosphorylation of PPARγ Affects the Collective Motions of the PPARγ-RXRα-DNA Complex. Plos One. 10: e0123984. PMID 25954810 DOI: 10.1371/journal.pone.0123984  0.84
2014 Lemkul JA, Savelyev A, MacKerell AD. Induced Polarization Influences the Fundamental Forces in DNA Base Flipping. The Journal of Physical Chemistry Letters. 5: 2077-2083. PMID 24976900 DOI: 10.1021/jz5009517  0.84
2014 Capelluto DG, Zhao X, Lucas A, Lemkul JA, Xiao S, Fu X, Sun F, Bevan DR, Finkielstein CV. Biophysical and molecular-dynamics studies of phosphatidic acid binding by the Dvl-2 DEP domain. Biophysical Journal. 106: 1101-11. PMID 24606934 DOI: 10.1016/j.bpj.2014.01.032  1
2014 Brown AM, Lemkul JA, Schaum N, Bevan DR. Simulations of monomeric amyloid β-peptide (1-40) with varying solution conditions and oxidation state of Met35: implications for aggregation. Archives of Biochemistry and Biophysics. 545: 44-52. PMID 24418316 DOI: 10.1016/j.abb.2014.01.002  0.84
2014 Gerben SR, Lemkul JA, Brown AM, Bevan DR. Comparing atomistic molecular mechanics force fields for a difficult target: a case study on the Alzheimer's amyloid β-peptide. Journal of Biomolecular Structure & Dynamics. 32: 1817-32. PMID 24028075 DOI: 10.1080/07391102.2013.838518  0.84
2013 Lemkul JA, Bevan DR. Aggregation of Alzheimer's amyloid β-peptide in biological membranes: a molecular dynamics study. Biochemistry. 52: 4971-80. PMID 23855340 DOI: 10.1021/bi400562x  1
2012 Lemkul JA, Bevan DR. The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease. Acs Chemical Neuroscience. 3: 845-56. PMID 23173066 DOI: 10.1021/cn300091a  1
2012 Lemkul JA, Bevan DR. Morin inhibits the early stages of amyloid β-peptide aggregation by altering tertiary and quaternary interactions to produce "off-pathway" structures. Biochemistry. 51: 5990-6009. PMID 22762350 DOI: 10.1021/bi300113x  1
2011 Lemkul JA, Bevan DR. Lipid composition influences the release of Alzheimer's amyloid β-peptide from membranes. Protein Science : a Publication of the Protein Society. 20: 1530-45. PMID 21692120 DOI: 10.1002/pro.678  1
2011 Lemkul JA, Bevan DR. Characterization of interactions between PilA from Pseudomonas aeruginosa strain K and a model membrane. The Journal of Physical Chemistry. B. 115: 8004-8. PMID 21630674 DOI: 10.1021/jp202217f  1
2010 Mehere P, Han Q, Lemkul JA, Vavricka CJ, Robinson H, Bevan DR, Li J. Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations. Protein & Cell. 1: 1023-32. PMID 21153519 DOI: 10.1007/s13238-010-0128-5  1
2010 Lemkul JA, Allen WJ, Bevan DR. Practical considerations for building GROMOS-compatible small-molecule topologies Journal of Chemical Information and Modeling. 50: 2221-2235. PMID 21117688 DOI: 10.1021/ci100335w  0.84
2010 Lemkul JA, Bevan DR. Destabilizing Alzheimer's Abeta(42) protofibrils with morin: mechanistic insights from molecular dynamics simulations. Biochemistry. 49: 3935-46. PMID 20369844 DOI: 10.1021/bi1000855  1
2010 Lemkul JA, Bevan DR. Assessing the stability of Alzheimer's amyloid protofibrils using molecular dynamics. The Journal of Physical Chemistry. B. 114: 1652-60. PMID 20055378 DOI: 10.1021/jp9110794  1
2009 Lemkul JA, Bevan DR. Perturbation of membranes by the amyloid beta-peptide--a molecular dynamics study. The Febs Journal. 276: 3060-75. PMID 19490108 DOI: 10.1111/j.1742-4658.2009.07024.x  1
2009 Allen WJ, Lemkul JA, Bevan DR. GridMAT-MD: A grid-based membrane analysis tool for use with molecular dynamics Journal of Computational Chemistry. 30: 1952-1958. PMID 19090582 DOI: 10.1002/jcc.21172  0.84
2008 Lemkul JA, Bevan DR. A comparative molecular dynamics analysis of the amyloid beta-peptide in a lipid bilayer. Archives of Biochemistry and Biophysics. 470: 54-63. PMID 18053791 DOI: 10.1016/j.abb.2007.11.004  1
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