Search Results - "Lopes, Pedro E. M"

A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids by Chowdhary, Janamejaya, Harder, Edward, Lopes, Pedro E. M, Huang, Lei, MacKerell, Alexander D, Roux, Benoît

“…A polarizable force field of saturated phosphatidylcholine-containing lipids based on the classical Drude oscillator model is optimized and used in molecular…”
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Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model by Huang, Jing, Lopes, Pedro E. M, Roux, Benoît, MacKerell, Alexander D

“…In this Perspective, we summarize recent efforts to include the explicit treatment of induced electronic polarization in biomolecular force fields. Methods…”
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Development of an Empirical Force Field for Silica. Application to the Quartz−Water Interface by Lopes, Pedro E. M, Murashov, Vladimir, Tazi, Mouhsine, Demchuk, Eugene, MacKerell, Alexander D

“…Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow…”
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Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator by Lopes, Pedro E. M, Lamoureux, Guillaume, Roux, Benoît, MacKerell, Alexander D

“…The polarizable empirical CHARMM force field based on the classical Drude oscillator has been extended to the aromatic compounds benzene and toluene…”
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Polarizable Empirical Force Field for Acyclic Polyalcohols Based on the Classical Drude Oscillator by He, Xibing, Lopes, Pedro E. M., MacKerell Jr, Alexander D.

“…ABSTRACT A polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator is presented. The model is optimized with an…”
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Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator by Harder, Edward, Anisimov, Victor M, Vorobyov, Igor V, Lopes, Pedro E. M, Noskov, Sergei Y, MacKerell, Alexander D, Roux, Benoît

“…Electron pairs in the valence shell of an atom that do not participate in the bonding of a molecule (“lone pairs”) give rise to a concentrated electron density…”
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Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields by Lin, Bin, Lopes, Pedro E M, Roux, Benoît, MacKerell, Jr, Alexander D

“…Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and…”
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Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator by Lin, Fang-Yu, Lopes, Pedro E. M, Harder, Edward, Roux, Benoît, MacKerell, Alexander D

“…Development of accurate force field parameters for molecular ions in the context of a polarizable energy function based on the classical Drude oscillator is a…”
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Intrinsic Energy Landscapes of Amino Acid Side-Chains by Zhu, Xiao, Lopes, Pedro E.M, Shim, Jihyun, MacKerell, Alexander D

“…Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions…”
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Current status of protein force fields for molecular dynamics simulations by Lopes, Pedro E M, Guvench, Olgun, MacKerell, Jr, Alexander D

“…The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and…”
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Recent developments and applications of the CHARMM force fields by Zhu, Xiao, Lopes, Pedro E. M., MacKerell Jr, Alexander D.

“…Empirical force fields (FFs) commonly used to describe the condensed‐phase properties of complex systems such as biological macromolecules are continuously…”
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Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field by Baker, Christopher M, Lopes, Pedro E. M, Zhu, Xiao, Roux, Benoît, MacKerell, Alexander D

“…Lennard-Jones (LJ) parameters for a variety of model compounds have previously been optimized within the CHARMM Drude polarizable force field to reproduce…”
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Six-site polarizable model of water based on the classical Drude oscillator by Yu, Wenbo, Lopes, Pedro E M, Roux, Benoît, MacKerell, Jr, Alexander D

“…A polarizable water model, SWM6, was developed and optimized for liquid phase simulations under ambient conditions. Building upon the previously developed…”
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Glucosylpolyphenols as Inhibitors of Aβ-Induced Fyn Kinase Activation and Tau Phosphorylation: Synthesis, Membrane Permeability, and Exploratory Target Assessment within the Scope of Type 2 Diabetes and Alzheimer’s Disease by de Matos, Ana M, Blázquez-Sánchez, M. Teresa, Bento-Oliveira, Andreia, de Almeida, Rodrigo F. M, Nunes, Rafael, Lopes, Pedro E. M, Machuqueiro, Miguel, Cristóvão, Joana S, Gomes, Cláudio M, Souza, Cleide S, El Idrissi, Imane G, Colabufo, Nicola A, Diniz, Ana, Marcelo, Filipa, Oliveira, M. Conceição, López, Óscar, Fernandez-Bolaños, José G, Dätwyler, Philipp, Ernst, Beat, Ning, Ke, Garwood, Claire, Chen, Beining, Rauter, Amélia P

“…Despite the rapidly increasing number of patients suffering from type 2 diabetes, Alzheimer’s disease, and diabetes-induced dementia, there are no…”
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Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa by Hom, Kellie, Heinzl, Geoffrey A, Eakanunkul, Suntara, Lopes, Pedro E. M, Xue, Fengtian, MacKerell, Alexander D, Wilks, Angela

“…Bacteria require iron for survival and virulence and employ several mechanisms including utilization of the host heme containing proteins. The final step in…”
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Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles by Best, Robert B, Zhu, Xiao, Shim, Jihyun, Lopes, Pedro E M, Mittal, Jeetain, Feig, Michael, Mackerell, Jr, Alexander D

“…While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the…”
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Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles by Best, Robert B, Zhu, Xiao, Shim, Jihyun, Lopes, Pedro E. M, Mittal, Jeetain, Feig, Michael, MacKerell, Alexander D

“…While the quality of the current CHARMM22/CMAP additive force field for proteins has been demonstrated in a large number of applications, limitations in the…”
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Holo-Ni(II)HpNikR Is an Asymmetric Tetramer Containing Two Different Nickel-Binding Sites by West, Abby L, St. John, Franz, Lopes, Pedro E. M, MacKerell, Alexander D, Pozharski, Edwin, Michel, Sarah L. J

“…The metalloregulatory protein NikR from Helicobacter pylori (HpNikR) is a master regulator of gene expression which both activates and represses specific genes…”
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Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator by Lopes, Pedro E. M, Huang, Jing, Shim, Jihyun, Luo, Yun, Li, Hui, Roux, Benoît, MacKerell, Alexander D

“…Presented is a polarizable force field based on a classical Drude oscillator framework, currently implemented in the programs CHARMM and NAMD, for modeling and…”
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Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications by Lopes, Pedro E. M., Roux, Benoit, MacKerell, Alexander D.

“…A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present…”
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