CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field J Lee, X Cheng, S Jo, AD MacKerell, JB Klauda, W Im Biophysical journal 110 (3), 641a, 2016 | 2863 | 2016 |
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 | 545 | 2016 |
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 | 475 | 2010 |
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 | 314 | 2009 |
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 | 227 | 2010 |
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 | 219 | 2016 |
Destabilizing Alzheimer’s Aβ42 Protofibrils with Morin: Mechanistic Insights from Molecular Dynamics Simulations JA Lemkul, DR Bevan Biochemistry 49 (18), 3935-3946, 2010 | 192 | 2010 |
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 | 110 | 2012 |
Lipid composition influences the release of Alzheimer's amyloid β‐peptide from membranes JA Lemkul, DR Bevan Protein Science 20 (9), 1530-1545, 2011 | 100 | 2011 |
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 | 96 | 2018 |
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 | 87 | 2014 |
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 | 83 | 2015 |
Perturbation of membranes by the amyloid β‐peptide–a molecular dynamics study JA Lemkul, DR Bevan The FEBS journal 276 (11), 3060-3075, 2009 | 83 | 2009 |
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 | 80 | 2017 |
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 | 80 | 2017 |
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 | 79 | 2008 |
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 | 78 | 2012 |
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 | 74 | 2018 |
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 | 71 | 2014 |
Aggregation of Alzheimer’s amyloid β-peptide in biological membranes: A molecular dynamics study JA Lemkul, DR Bevan Biochemistry 52 (29), 4971-4980, 2013 | 64 | 2013 |