| Year |
Citation |
Score |
| 2024 |
Davidson DS, Lemkul JA. Pyroglutamylation modulates electronic properties and the conformational ensemble of the amyloid β-peptide. Proteins. PMID 38436541 DOI: 10.1002/prot.26677 |
0.794 |
|
| 2023 |
Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. Journal of Chemical Information and Modeling. 63: 6851-6862. PMID 37847037 DOI: 10.1021/acs.jcim.3c01305 |
0.754 |
|
| 2023 |
Polêto MD, Lemkul JA. Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes. Biorxiv : the Preprint Server For Biology. PMID 37645825 DOI: 10.1101/2023.08.10.552810 |
0.758 |
|
| 2023 |
Wacha AF, Lemkul JA. charmm2gmx: An Automated Method to Port the CHARMM Additive Force Field to GROMACS. Journal of Chemical Information and Modeling. PMID 37399236 DOI: 10.1021/acs.jcim.3c00860 |
0.446 |
|
| 2023 |
Giacon N, Lo Cascio E, Davidson DS, Polêto MD, Lemkul JA, Pennacchietti V, Pagano L, Zamparelli C, Toto A, Arcovito A. Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein. Computational and Structural Biotechnology Journal. 21: 3259-3271. PMID 37293240 DOI: 10.1016/j.csbj.2023.05.027 |
0.782 |
|
| 2022 |
Davidson DS, Kraus JA, Montgomery JM, Lemkul JA. 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. PMID 36150020 DOI: 10.1021/acs.jpcb.2c03520 |
0.801 |
|
| 2022 |
Salsbury AM, Michel HM, Lemkul JA. Ion-Dependent Conformational Plasticity of Telomeric G-Hairpins and G-Quadruplexes. Acs Omega. 7: 23368-23379. PMID 35847338 DOI: 10.1021/acsomega.2c01600 |
0.771 |
|
| 2022 |
Corrigan AN, Lemkul JA. Electronic Polarization at the Interface between the p53 Transactivation Domain and Two Binding Partners. The Journal of Physical Chemistry. B. PMID 35749260 DOI: 10.1021/acs.jpcb.2c02268 |
0.808 |
|
| 2022 |
Polêto MD, Lemkul JA. TUPÃ: Electric field analyses for molecular simulations. Journal of Computational Chemistry. PMID 35460102 DOI: 10.1002/jcc.26873 |
0.758 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2022 |
Polêto MD, Lemkul JA. Integration of Experimental Data and Use of Automated Fitting Methods in Developing Protein Force Fields. Communications Chemistry. 5. PMID 35382231 DOI: 10.1038/s42004-022-00653-z |
0.856 |
|
| 2021 |
King KM, Sharp AK, Davidson DS, Brown AM, Lemkul JA. Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogenous Amyloid Oligomers. Journal of Computational Biophysics and Chemistry. 21: 449-460. PMID 35756548 DOI: 10.1142/s2737416521420059 |
0.789 |
|
| 2021 |
Kognole AA, Lee J, Park SJ, Jo S, Chatterjee P, Lemkul JA, Huang J, MacKerell AD, Im W. CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. Journal of Computational Chemistry. PMID 34874077 DOI: 10.1002/jcc.26795 |
0.829 |
|
| 2021 |
Lemkul JA. Preparing and Analyzing Polarizable Molecular Dynamics Simulations with the Classical Drude Oscillator Model. Methods in Molecular Biology (Clifton, N.J.). 2315: 219-240. PMID 34302679 DOI: 10.1007/978-1-0716-1468-6_13 |
0.415 |
|
| 2021 |
Salsbury AM, Lemkul JA. Cation Competition and Recruitment around the c-kit1 G-Quadruplex Using Polarizable Simulations. Biophysical Journal. PMID 33794153 DOI: 10.1016/j.bpj.2021.03.022 |
0.788 |
|
| 2020 |
Ratnasinghe BD, Salsbury AM, Lemkul JA. Ion Binding Properties and Dynamics of the 2 G-Quadruplex Using a Polarizable Force Field. Journal of Chemical Information and Modeling. PMID 33264004 DOI: 10.1021/acs.jcim.0c01064 |
0.815 |
|
| 2020 |
Salsbury AM, Lemkul JA. Recent developments in empirical atomistic force fields for nucleic acids and applications to studies of folding and dynamics. Current Opinion in Structural Biology. 67: 9-17. PMID 32950937 DOI: 10.1016/J.Sbi.2020.08.003 |
0.823 |
|
| 2020 |
Salsbury A, Dean T, Lemkul JA. 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. PMID 32307997 DOI: 10.1021/Acs.Jctc.0C00191 |
0.802 |
|
| 2020 |
Lemkul JA. Pairwise-additive and polarizable atomistic force fields for molecular dynamics simulations of proteins. Progress in Molecular Biology and Translational Science. 170: 1-71. PMID 32145943 DOI: 10.1016/Bs.Pmbts.2019.12.009 |
0.629 |
|
| 2020 |
Dean T, Salsbury AM, Lemkul JA. Dynamics of the 1:2:1 and 1:6:1 C-Myc G-Quadruplexes with the Drude Polarizable Force Field Biophysical Journal. 118: 65a. DOI: 10.1016/J.Bpj.2019.11.533 |
0.489 |
|
| 2020 |
Lemkul JA. Polarizable Molecular Dynamics Simulations of DNA G-Quadruplexes Reveal Different Properties of Nucleobase Electronic Structure and Cation Binding Biophysical Journal. 118: 220a. DOI: 10.1016/J.Bpj.2019.11.1307 |
0.351 |
|
| 2020 |
Salsbury AM, Lemkul JA. Influence of Monovalent Cations on the Dynamics of the C-KIT1 Promoter G-Quadruplex using Polarizable Molecular Dynamics Simulations Biophysical Journal. 118: 220a. DOI: 10.1016/J.Bpj.2019.11.1305 |
0.335 |
|
| 2019 |
Lemkul JA. Same fold, different properties: polarizable molecular dynamics simulations of telomeric and TERRA G-quadruplexes. Nucleic Acids Research. PMID 31807754 DOI: 10.1093/Nar/Gkz1154 |
0.442 |
|
| 2019 |
Pawlak R, Vilhena JG, D'Astolfo P, Liu X, Prampolini G, Meier T, Glatzel T, Lemkul JA, Häner R, Decurtins S, Baratoff A, Pérez R, Liu SX, Meyer E. Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer. Nano Letters. PMID 31797665 DOI: 10.1021/Acs.Nanolett.9B04418 |
0.442 |
|
| 2019 |
Hollingsworth LR, Lemkul JA, Gandour RD, Bevan DR, Brown AM. Molecular Dynamics Simulations of gp120 and gp41 of HIV Env Provide Insights into Strain Specificity and the Role of the Membrane Environment Biophysical Journal. 116: 46a. DOI: 10.1016/J.Bpj.2018.11.293 |
0.717 |
|
| 2019 |
Salsbury AM, Lemkul JA. Polarizable Molecular Dynamics Simulations of C-Kit Oncogene Promoter G-Quadruplexes of Distinct Conformations Biophysical Journal. 116: 360a. DOI: 10.1016/J.Bpj.2018.11.1959 |
0.343 |
|
| 2019 |
Ratnasinghe BD, Salsbury AM, Porier DL, Lemkul JA. Structure and Dynamics of the Bcl-2 Promoter G-Quadruplex using the Drude Polarizable Force Field Biophysical Journal. 116: 359a. DOI: 10.1016/J.Bpj.2018.11.1954 |
0.51 |
|
| 2019 |
Davidson DS, Lemkul JA. Investigating the Role of Charge-Altering Post-Translational Modifications on Tau Peptide Conformational Ensembles using Polarizable Molecular Dynamics Simulations Biophysical Journal. 116: 199a. DOI: 10.1016/J.Bpj.2018.11.1103 |
0.345 |
|
| 2018 |
Salsbury AM, Lemkul JA. 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. PMID 30525627 DOI: 10.1021/Acs.Jpcb.8B11026 |
0.837 |
|
| 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 |
0.658 |
|
| 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 |
0.504 |
|
| 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 |
0.738 |
|
| 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 |
0.822 |
|
| 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 |
0.647 |
|
| 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 |
0.497 |
|
| 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 |
0.688 |
|
| 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 |
0.658 |
|
| 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 |
0.466 |
|
| 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 |
0.626 |
|
| 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 |
0.605 |
|
| 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 |
0.703 |
|
| 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 |
0.605 |
|
| 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 |
0.581 |
|
| 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 |
0.55 |
|
| 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 |
0.644 |
|
| 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 |
0.749 |
|
| 2015 |
Lemkul JA, Savelyev A, MacKerell AD. Towards a Polarizable Force Field for RNA based on the Classical Drude Oscillator Biophysical Journal. 108: 159a. DOI: 10.1016/J.Bpj.2014.11.875 |
0.444 |
|
| 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 |
0.6 |
|
| 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 |
0.593 |
|
| 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 |
0.742 |
|
| 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 |
0.803 |
|
| 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 |
0.585 |
|
| 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 |
0.64 |
|
| 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 |
0.618 |
|
| 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 |
0.582 |
|
| 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 |
0.601 |
|
| 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 |
0.585 |
|
| 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 |
0.726 |
|
| 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 |
0.6 |
|
| 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 |
0.601 |
|
| 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 |
0.587 |
|
| 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 |
0.607 |
|
| 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 |
0.593 |
|
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