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Items: 34

1.

Small Molecule Thermochemistry: A Tool for Empirical Force Field Development.

van der Spoel D, Ghahremanpour MM, Lemkul JA.

J Phys Chem A. 2018 Nov 6. doi: 10.1021/acs.jpca.8b09867. [Epub ahead of print]

PMID:
30362355
2.

Erratum for Sanders et al., "FusoPortal: an Interactive Repository of Hybrid MinION-Sequenced Fusobacterium Genomes Improves Gene Identification and Characterization".

Sanders BE, Umana A, Lemkul JA, Slade DJ.

mSphere. 2018 Jul 25;3(4). pii: e00379-18. doi: 10.1128/mSphere.00379-18. No abstract available.

3.

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

Sanders BE, Umana A, Lemkul JA, Slade DJ.

mSphere. 2018 Jul 5;3(4). pii: e00228-18. doi: 10.1128/mSphere.00228-18. Erratum in: mSphere. 2018 Jul 25;3(4):.

4.

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

Hollingsworth LR 4th, Lemkul JA, Bevan DR, Brown AM.

Biophys J. 2018 Jul 3;115(1):84-94. doi: 10.1016/j.bpj.2018.05.022.

PMID:
29972814
5.

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

Davidson DS, Brown AM, Lemkul JA.

J Mol Biol. 2018 Oct 12;430(20):3819-3834. doi: 10.1016/j.jmb.2018.05.020. Epub 2018 May 18.

PMID:
29782833
6.

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

Huang J, Lemkul JA, Eastman PK, MacKerell AD Jr.

J Comput Chem. 2018 Aug 5;39(21):1682-1689. doi: 10.1002/jcc.25339. Epub 2018 May 4.

PMID:
29727037
7.

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

Klontz EH, Tomich AD, Günther S, Lemkul JA, Deredge D, Silverstein Z, Shaw JF, McElheny C, Doi Y, Wintrode PL, MacKerell AD Jr, Sluis-Cremer N, Sundberg EJ.

Antimicrob Agents Chemother. 2017 Oct 24;61(11). pii: e01572-17. doi: 10.1128/AAC.01572-17. Print 2017 Nov.

8.

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

Lemkul JA, MacKerell AD Jr.

J Chem Theory Comput. 2017 May 9;13(5):2053-2071. doi: 10.1021/acs.jctc.7b00067. Epub 2017 Apr 19.

9.

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

Lemkul JA, MacKerell AD Jr.

J Chem Theory Comput. 2017 May 9;13(5):2072-2085. doi: 10.1021/acs.jctc.7b00068. Epub 2017 Apr 19.

10.

Characterization of Mg2+ Distributions around RNA in Solution.

Lemkul JA, Lakkaraju SK, MacKerell AD Jr.

ACS Omega. 2016 Oct 31;1(4):680-688. Epub 2016 Oct 26.

11.
12.

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

Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL 3rd, MacKerell AD Jr.

Bioorg Med Chem. 2016 Oct 15;24(20):4812-4825. doi: 10.1016/j.bmc.2016.06.034. Epub 2016 Jun 18.

13.

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

Lemkul JA, Huang J, Roux B, MacKerell AD Jr.

Chem Rev. 2016 May 11;116(9):4983-5013. doi: 10.1021/acs.chemrev.5b00505. Epub 2016 Jan 27. Review.

14.

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field.

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 3rd, MacKerell AD Jr, Klauda JB, Im W.

J Chem Theory Comput. 2016 Jan 12;12(1):405-13. doi: 10.1021/acs.jctc.5b00935. Epub 2015 Dec 3.

15.

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

Lemkul JA, Huang J, MacKerell AD Jr.

J Phys Chem B. 2015 Dec 24;119(51):15574-82. doi: 10.1021/acs.jpcb.5b09978. Epub 2015 Dec 15.

16.

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

Lakkaraju SK, Lemkul JA, Huang J, MacKerell AD Jr.

J Comput Chem. 2016 Feb 5;37(4):416-25. doi: 10.1002/jcc.24231. Epub 2015 Nov 12.

17.

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

Lemkul JA, Roux B, van der Spoel D, MacKerell AD Jr.

J Comput Chem. 2015 Jul 15;36(19):1473-9. doi: 10.1002/jcc.23937. Epub 2015 May 12.

18.

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

Lemkul JA, Lewis SN, Bassaganya-Riera J, Bevan DR.

PLoS One. 2015 May 8;10(5):e0123984. doi: 10.1371/journal.pone.0123984. eCollection 2015.

19.

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping.

Lemkul JA, Savelyev A, MacKerell AD Jr.

J Phys Chem Lett. 2014 Jun 19;5(12):2077-2083. Epub 2014 May 28.

20.

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

Capelluto DG, Zhao X, Lucas A, Lemkul JA, Xiao S, Fu X, Sun F, Bevan DR, Finkielstein CV.

Biophys J. 2014 Mar 4;106(5):1101-11. doi: 10.1016/j.bpj.2014.01.032.

21.

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

Brown AM, Lemkul JA, Schaum N, Bevan DR.

Arch Biochem Biophys. 2014 Mar 1;545:44-52. doi: 10.1016/j.abb.2014.01.002. Epub 2014 Jan 11.

PMID:
24418316
22.

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

Gerben SR, Lemkul JA, Brown AM, Bevan DR.

J Biomol Struct Dyn. 2014;32(11):1817-32. doi: 10.1080/07391102.2013.838518. Epub 2013 Sep 13.

PMID:
24028075
23.

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

Lemkul JA, Bevan DR.

Biochemistry. 2013 Jul 23;52(29):4971-80. doi: 10.1021/bi400562x. Epub 2013 Jul 15.

PMID:
23855340
24.

The role of molecular simulations in the development of inhibitors of amyloid β-peptide aggregation for the treatment of Alzheimer's disease.

Lemkul JA, Bevan DR.

ACS Chem Neurosci. 2012 Nov 21;3(11):845-56. doi: 10.1021/cn300091a. Epub 2012 Aug 27. Review.

25.
26.

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

Lemkul JA, Bevan DR.

Protein Sci. 2011 Sep;20(9):1530-45. doi: 10.1002/pro.678. Epub 2011 Jul 13.

27.

Characterization of interactions between PilA from Pseudomonas aeruginosa strain K and a model membrane.

Lemkul JA, Bevan DR.

J Phys Chem B. 2011 Jun 23;115(24):8004-8. doi: 10.1021/jp202217f. Epub 2011 Jun 1.

PMID:
21630674
28.

Tyrosine aminotransferase: biochemical and structural properties and molecular dynamics simulations.

Mehere P, Han Q, Lemkul JA, Vavricka CJ, Robinson H, Bevan DR, Li J.

Protein Cell. 2010 Nov;1(11):1023-32. doi: 10.1007/s13238-010-0128-5. Epub 2010 Dec 10.

29.

Practical considerations for building GROMOS-compatible small-molecule topologies.

Lemkul JA, Allen WJ, Bevan DR.

J Chem Inf Model. 2010 Dec 27;50(12):2221-35. doi: 10.1021/ci100335w. Epub 2010 Nov 30.

PMID:
21117688
30.

Destabilizing Alzheimer's Abeta(42) protofibrils with morin: mechanistic insights from molecular dynamics simulations.

Lemkul JA, Bevan DR.

Biochemistry. 2010 May 11;49(18):3935-46. doi: 10.1021/bi1000855.

PMID:
20369844
31.

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

Lemkul JA, Bevan DR.

J Phys Chem B. 2010 Feb 4;114(4):1652-60. doi: 10.1021/jp9110794.

PMID:
20055378
32.

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

Lemkul JA, Bevan DR.

FEBS J. 2009 Jun;276(11):3060-75. doi: 10.1111/j.1742-4658.2009.07024.x. Epub 2009 Apr 22.

33.

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

Allen WJ, Lemkul JA, Bevan DR.

J Comput Chem. 2009 Sep;30(12):1952-8. doi: 10.1002/jcc.21172.

PMID:
19090582
34.

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

Lemkul JA, Bevan DR.

Arch Biochem Biophys. 2008 Feb 1;470(1):54-63. Epub 2007 Nov 17.

PMID:
18053791

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