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Molecular dynamics simulation

Tìm thấy 10+ kết quả cho từ khóa "Molecular dynamics simulation"

Molecular docking analysis and molecular dynamics simulation study of ameltolide analogous as a sodium channel blocker

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Abstract:Fifteen compounds related to ameltolide with sodium channel inhibitory activity were subjected to a molecular docking study. To confirm the binding mode of inhibitors, molecular dynamics simulations were performed using GROMACS 4.5.5, based upon the docked conformation of ameltolide.

A new formulation for fast calculation of far field force in molecular dynamics simulations

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A new formulation for fast calculation of far field force in molecular dynamics simulations. We have developed a new formulation for fast calculation of far-field force of fast multipole method (FMM)in molecular dynamics simulations. GRAPE is a special-purpose computer dedicated to Coulombic force calculation. However FMM cannot be implemented directly on GRAPE. We have succeeded to implement FMM on GRAPE and developed a new formulation for far-field force calculation.

Pore length- and ion concentration-dependent ionic current in cylindrical nanopores: An atomistic molecular dynamics study

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Here we present atomistic molecular dynamics simulation results from colloidal nanoparticle translocation through mid-to-low aspect ratio charged nanopores under an external field.

Integrated 3D-QSAR, molecular docking, and molecular dynamics simulation studies on 1,2,3-triazole based derivatives for designing new acetylcholinesterase inhibitors

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These virtual structures were subjected to 20 ns MD simulations to study the comparative conformation dynamics of the protein after ligand binding. Energy, temperature, pressure, and density of the compound bound protein were stable during the 20 ns simulation. The analysis provides insights into protein conformation, stability, and equilibrium of the system during simulation [37].

A simulation study of the amorphous germania structure up to 70 GPa

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A Simulation Study of the Amorphous Germania Structure up to 70 GPa. The Molecular Dynamics simulation was performed on systems at 900 K and high pressure up to 70 GPa. The structural properties have been analyzed through the pair correlation function, coordination number distribution, and structure factors. Correlation between the peaks in the plot of structure factor and the topology of basic structural units GeO n (n = 4-6) is also discussed in detail in this paper..

The influence of temperature on the microstructure and the phase transition process of the SiO2 bulk model

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To study the microstructure and the phase transition process of SiO 2 by the Molecular Dynamics (MD) Simulation method, pair interaction potential and the van Beest-Kramer- van Santen (BKS) pair interaction potential were used [17], in which we mainly used the BKS pair interaction potential. In this paper, we used the Molecular Dynamics Simulation method with BKS pair interaction potential in the form (1) and periodic boundary conditions..

Combined ligand and structure-based virtual screening approaches for identification of novel AChE inhibitors

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Modulation in the conformational and stability attributes of the Alzheimer’s disease associated amyloid-beta mutants and their favorable stabilization by curcumin: molecular dynamics simulation analysis. International Journal of Biological Macro- molecules 2017. Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Journal of Chemical Information and Modeling 2016. Journal of Molecular Graphics and Modelling 2014. Journal of Computational Chemistry 2005.

Exploring distinct binding site regions of β2-adrenergic receptor via coarse-grained molecular dynamics simulations

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Statistical analyses of the experimental structures were used for developing the force field of the 2-bead models. 19,20 The model was employed to investigate the molecular basis of how the physicochemical properties of the phospholipid bilayer membrane affect self-assembly of visual rhodopsin molecules, which are members of the G protein-coupled receptor.

Why protein conformers in molecular dynamics simulations differ from their crystal structures: A thermodynamic insight

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Interestingly, it happens that changes in RMSDs during the first 2 orders of magnitude in MD simulation time, from 10 − 2 ns to 10 0 ns, are qualitatively comparable with those happening in the following 2 orders of magnitude in simulation time, from 10 0 ns to 10 2 ns (see Figure 4). This behavior suggests that the RMSDs in the first 10 ns of simulation are not simply a result of the equilibrium fluctuations.

Linkage of nanosecond protein motion with enzymatic methyl transfer by nicotinamide N-methyltransferase

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Advanced techniques for characterizing dynamic properties including nuclear magnetic resonance (NMR) (Nodet and Abergel, 2007), fluorescence spectroscopy (Lakowicz, 1999), molecular dynamics simulation (Karplus and Kuriyan, 2005), and X-ray crystallography (Srajer et al., 1996). Here, nicotinamide N-methyltransferase and its mutants were selected and combed with enzyme activity and protein fluorescence measurements to explore the relationship between protein dynamics and protein function..

Interaction of camel Lactoferrin derived peptides with DNA: A molecular dynamics study

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Molecular dynamics simulation in aqueous solution of the isolated peptides and BDNA. The Ramachandran plot for CLFampin, CLFcin and CLFchimera revealed that and 93.5% of the residues were situated within the most favored region, respectively, whereas the remaining residues were found within the additional allowed region..

The Structure of Liquid PbSiO3: Insight from Analysis and Visualization of Molecular Dynamics Data

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Mancini, The structure of lead-silicate glasses: molecular dynamics and EXAFS studies, J. [16] Valle R G D and Venuti E, High-pressure densification of silica glass: A molecular-dynamics simulation, Phys.. J.C and Della Mea G, Physical properties of lead-silicate glassy thin films deposited by sputtering in Ar : H 2 mixtures, Nuc. R Corrales, Sensitivity of structural results to initial configurations and quench algorithms of lead silicate glass, J

Evaluation of quercetin as a potential β-lactamase CTX-M-15 inhibitor via the molecular docking, dynamics simulations, and MMGBSA

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Molecular dynamics simulations of CTX-M-15-ligand complexes. The complexes of avibactam, sulbactam, clavulanic acid, tazobactam, and quercetin were docked to target protein CTX- M-15 were simulated for 100 ns by molecular dynamics methods to reveal information about whether the ligands docked at the target molecule remained stable at the initial binding position.

Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare)

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Wild-type Pre-simulation . Variant II Pre-simulation .

Molecular dynamics simulations of adsorption of long pyrene-PEG chains on a thin carbon nanotube

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The focus was on the effect of chain molecular weight on their adsorption rate over a CNT surface using full-atom MD simulations.. In addition, diffusional behaviors of both adsorbed and free pyrene molecules attached to long PEG chains were analyzed. The dynamics of PEG chains were also investigated to reveal their effect on the adsorption process..

Computational analysis of the receptor binding specificity of novel influenza A/H7N9 viruses

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Molecular dynamics simulation reveals residues that contribute to enhanced binding of HA protein with host cell receptors. To observe the dynamic HA-receptor interaction and compare the change of interaction energy induced by sub- stitutions on the protein, we conducted molecular dynam- ics simulation for the HA proteins to form complexes with receptor analogs. In addition, the mutations enhanced binding of HA protein with both LSTa and LSTc.

Structural analysis of plasmid-mediated verotoxin gene producing non-O157 escherichia coli using molecular dynamic simulations

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Molecular dynamics refine the structure of the proteins and shapes a group of conformities to their native state. (Raval et al., 2012). Hence, the stability of the Vtx structure was estimated as a function of simulation time. Consequently, Vtx2 reached a plateau state at around 2.0 Å after 10 ns and consistently deviated between 2 Å-2.5 Å until the end of the simulation. Furthermore, the radius of gyration was evaluated for the stability of the Vtx models.

Handbook of Micro and Nano Tribology P11

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A Comparison of the Structure and Solvation Forces Using Molecular Dynamics,” J

An integrated program to simulate the multibody dynamics of flapping flight

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However, it should be noted that in that study, the aerodynamics solver is not entirely coupled with the iterations of the dynamics solver. Instead, the aerodynamic force is calculated for each time step, and this force is assumed to be constant during the iterations of the dynamics solver. This study presents the first attempt to entirely couple the unsteady aerodynamics solver with a multibody dynamics code.. MSC Adams uses the GSTIFF solver for the multibody dynamics simulation.

The single nucleotide β -arrestin2 variant, A248T, resembles dynamical properties of activated arrestin

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Structure and dynamics of the TIP3P, SPC, and SPC/E water models at 298 K. Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. X-ray laser diffraction for structure determination of the