Listar por tema "molecular dynamics"
Mostrando ítems 1-20 de 35
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AMPA receptor GluA2 subunit defects are a cause of neurodevelopmental disorders
(2019)AMPA receptors (AMPARs) are tetrameric ligand-gated channels made up of combinations of GluA1-4 subunits encoded by GRIA1-4 genes. GluA2 has an especially important role because, following post-transcriptional editing at ... -
Aqueous Solubility Enhancement for Bioassays of Insoluble Inhibitors and QSPR Analysis: A TNF-α Study
(2018)The aim of this study is to improve the aqueous solubility of a group of compounds without interfering with their bioassay as well as to create a relevant prediction model. A series of 55 potential small-molecule inhibitors ... -
Cation adatom diffusion on the NiO(001) surface by molecular dynamics simulation
(2001)We present results concerning the diffusion of Ni2+ adatom on the (001) surface of NiO obtained by molecular dynamics simulations based on a rigid ion potential model. A wide temperature region was covered ranging from ... -
Cation vacancy diffusion on the NiO(001) surface by molecular dynamics simulations
(1999)We present results concerning the cation vacancy diffusion mechanisms occurring on the NiO(001) surface along with their corresponding migration energies. Using a rigid ion potential and molecular dynamics simulations we ... -
Changes in the level of poly(Phe) synthesis in Escherichia coli ribosomes containing mutants of L4 ribosomal protein from Thermus thermophilus can be explained by structural changes in the peptidyltransferase center: a molecular dynamics simulation analysis
(2006)Data from polyphenylalanine [poly(Phe)] synthesis determination in the presence and in the absence of erythromycin have been used in conjunction with Molecular Dynamics Simulation analysis, in order to localize the functional ... -
Cheminformatics-aided discovery of small-molecule Protein-Protein Interaction (PPI) dual inhibitors of Tumor Necrosis Factor (TNF) and Receptor Activator of NF-κB Ligand (RANKL)
(2017)We present an in silico drug discovery pipeline developed and applied for the identification and virtual screening of small-molecule Protein-Protein Interaction (PPI) compounds that act as dual inhibitors of TNF and RANKL ... -
Current status and future prospects of small–molecule protein–protein interaction (PPI) inhibitors of tumor necrosis factor (TNF) and receptor activator of NF-κB ligand (RANKL)
(2018)The overexpression of Tumor Necrosis Factor (TNF) is directly related to the development of several autoimmune diseases, such as rheumatoid and psoriatic arthritis, inflammatory bowel disease, Crohn’s disease, refractory ... -
Design and Synthesis of Type-IV Inhibitors of BRAF Kinase That Block Dimerization and Overcome Paradoxical MEK/ERK Activation
(2019)Despite the clinical success of BRAF inhibitors like vemurafenib in treating metastatic melanoma, resistance has emerged through "paradoxical MEK/ERK signaling" where transactivation of one protomer occurs as a result of ... -
Determination of the number of water molecules in the proton pathway of bacteriorhodopsin using neutron diffraction data
(2003)It has been shown that water molecules participate in the proton pathway of bacteriorhodopsin. Large efforts have been made to determine with various biophysical methods the number of water molecules involved. Neutron ... -
Discovery of Small-Molecule Inhibitors of Receptor Activator of Nuclear Factor-κB Ligand with a Superior Therapeutic Index
(2020)Receptor activator of nuclear factor-κB ligand (RANKL) constitutes the master mediator of osteoclastogenesis, while its pharmaceutical inhibition by a monoclonal antibody has been approved for the treatment of postmenopausal ... -
Effects of wall roughness on flow in nanochannels
(2009)Nonequilibrium molecular dynamics simulation is applied to investigate the effect of periodic wall roughness on the flow of liquid argon through krypton nanochannels. The effect of the length of a rectangular protrusion ... -
Elastic properties of nanostructured materials with layered grain boundary structure
(2007)Atomistic calculations of the elastic constants for a bulk nanostructured material that consists of a layered structure where alternating layers meet along high angle grain boundaries and where atoms interact via a ... -
Emergence of sequence type 11 Klebsiella pneumoniae coproducing NDM-1 and VIM-1 metallo-β-lactamases in a Greek hospital
(2017)Sequence type 11 Klebsiella pneumoniae, coproducing NDM-1 and VIM-1 metallo-β-lactamases, were isolated in a Greek hospital. blaNDM-1 was part of a Tn125 derivative, located on an ~90-kb plasmid similar to the NDM-1-encoding ... -
Emerging molecular networks common in ionizing radiation, immune and inflammatory responses by employing bioinformatics approaches
(2015)Efficient radiation therapy is characterized by enhanced tumor cell killing involving the activation of the immune system (tumor immunogenicity) but at the same time minimizing chronic inflammation and radiation adverse ... -
Evidence for Novel Action at the Cell-Binding Site of Human Angiogenin Revealed by Heteronuclear NMR Spectroscopy, in silico and in vivo Studies
(2018)A member of the ribonuclease A superfamily, human angiogenin (hAng) is a potent angiogenic factor. Heteronuclear NMR spectroscopy combined with induced-fit docking revealed a dual binding mode for the most antiangiogenic ... -
The expression of myeloproliferative neoplasm-associated calreticulin variants depends on the functionality of er-associated degradation
(2019)Background: Mutations in CALR observed in myeloproliferative neoplasms (MPN) were recently shown to be pathogenic via their interaction with MPL and the subsequent activation of the Janus Kinase – Signal Transducer and ... -
Fluid ordering effects and density variations in nanochannel flows: a quasicontinuum theory
(2014)A quasicontinuum self-diffusion theory that can capture the fluid ordering effects and density variations predicted by nonequilibrium molecular dynamics in nanochannel flows is presented. The physics of the problem suggests ... -
Frequency dependent non-thermal effects of oscillating electric fields in the microwave region on the properties of a solvated lysozyme system: A molecular dynamics study
(2017)The use of microwaves in every day's applications raises issues regarding the non thermal biological effects of microwaves. In this work we employ molecular dynamics simulations to advance further the dielectric studies ... -
In silico study of levodopa in hydrated lipid bilayers at the atomistic level
(2021)This article presents atomistic molecular dynamics and umbrella sampling simulations of levodopa at various concentrations in hydrated cholesterol-free 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and cholesterol-containing ... -
Insights into the molecular etiology of exercise-induced inflammation: Opportunities for optimizing performance
(2016)The study of exercise-induced muscle damage (EIMD) is of paramount importance not only because it affects athletic performance but also because it is an excellent model to study the mechanisms governing muscle cachexia ...