Polarizable Empirical Force Field for Nitrogen-containing Heteroaromatic Compounds Based on the Classical Drude Oscillator

di Lopes, Pedro E. M., Lamoureux, Guillaume, MacKerell, Alexander D.
Pubblicazione 2009

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

di Lopes, Pedro E. M., Roux, Benoit, MacKerell, Alexander D.
Pubblicazione 2009

Recent Developments and Applications of the CHARMM force fields

di Zhu, Xiao, Lopes, Pedro E.M., MacKerell, Alexander D.
Pubblicazione 2011

Polarizable Empirical Force Field for Acyclic Poly-Alcohols Based on the Classical Drude Oscillator

di He, Xibing, Lopes, Pedro E. M., MacKerell, Alexander D.
Pubblicazione 2013

Current Status of Protein Force Fields for Molecular Dynamics

di Lopes, Pedro E.M., Guvench, Olgun, MacKerell, Alexander D.
Pubblicato in Methods Mol Biol (2015)

Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator

di Lopes, Pedro E. M., Lamoureux, Guillaume, Roux, Benoit, MacKerell, Alexander D.
Pubblicazione 2007

Intrinsic energy landscapes of amino acid side chains

di Zhu, Xiao, Lopes, Pedro E.M., Shim, Jihyun, MacKerell, Alexander D.
Pubblicazione 2012

Six-site polarizable model of water based on the classical Drude oscillator

di Yu, Wenbo, Lopes, Pedro E. M., Roux, Benoît, MacKerell, Alexander D.
Pubblicazione 2013

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields

di Lin, Bin, Lopes, Pedro E. M., Roux, Benoît, MacKerell, Alexander D.
Pubblicazione 2013

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

di Huang, Jing, Lopes, Pedro E. M., Roux, Benoît, MacKerell, Alexander D.
Pubblicazione 2014

Development of an Empirical Force Field for Silica. Application to the Quartz-Water Interface

di Lopes, Pedro E. M., Murashov, Vladimir, Tazi, Mouhsine, Demchuk, Eugene, MacKerell, Alexander D.
Pubblicazione 2006

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field

di Baker, Christopher M., Lopes, Pedro E. M., Zhu, Xiao, Roux, Benoît, MacKerell, Alexander D.
Pubblicazione 2010

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

di Lin, Fang-Yu, Lopes, Pedro E. M., Harder, Edward, Roux, Benoît, MacKerell, Alexander D.
Pubblicato in J Chem Inf Model (2018)

A Polarizable Force Field of Dipalmitoylphosphatidylcholine based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids

di Chowdhary, Janamejaya, Harder, Edward, Lopes, Pedro E. M., Huang, Lei, MacKerell, Alexander D., Roux, Benoît
Pubblicazione 2013

Force Field for Peptides and Proteins based on the Classical Drude Oscillator

di Lopes, Pedro E.M., Huang, Jing, Shim, Jihyun, Luo, Yun, Li, Hui, Roux, Benoît, MacKerell, Alexander D.
Pubblicazione 2013

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

di Best, Robert B., Zhu, Xiao, Shim, Jihyun, Lopes, Pedro E. M., Mittal, Jeetain, Feig, Michael, MacKerell, Alexander D.
Pubblicazione 2012

Small Molecule Antivirulents Targeting the Iron-Regulated Heme Oxygenase (HemO) of P. aeruginosa

di Hom, Kellie, Heinzl, Geoffrey A., Eakanunkul, Suntara, Lopes, Pedro E. M., Xue, Fengtian, MacKerell, Alexander D., Wilks, Angela
Pubblicazione 2013

Holo-Ni(II)HpNikR is an asymmetric tetramer containing two different nickel binding sites

di West, Abby L., John, Franz St., Lopes, Pedro E. M., MacKerell, Alexander D., Pozharski, Ed, Michel, Sarah L.J.
Pubblicazione 2010

The small molecule IMR-1 inhibits the Notch transcriptional activation complex to suppress tumorigenesis

di Astudillo, Luisana, Da Silva, Thiago G., Wang, Zhiqiang, Han, Xiaoqing, Jin, Ke, VanWye, Jeffrey, Zhu, Xiaoxia, Weaver, Kelly, Oashi, Taiji, Lopes, Pedro E.M., Orton, Darren, Neitzel, Leif R., Lee, Ethan, Landgraf, Ralf, Robbins, David J, MacKerell, Alexander D., Capobianco, Anthony J.
Pubblicato in Cancer Res (2016)