نتایج جستجو برای: gromacs software
تعداد نتایج: 437470 فیلتر نتایج به سال:
The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energy ΔG(bind) of oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus. ΔG(bind) is estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinati...
The fundamental problems in drug discovery are based on the process of molecular recognition by small molecules. The binding specificity of DNA-small molecule is identified mainly by studying the hydrogen bonding and polar interactions. Majority of the minor groove binders and their mechanism of action at the molecular level are not well studied. As these small molecules can act as effective th...
The approximative density-functional method DFTB3 has been implemented in the Gromacs package version 5, complementing the existing QM/MM interface. The tight integration within the program gives rise to favorable efficiency, and makes it possible to employ a full PME-based treatment of QM/MM electrostatic interaction. Therefore, unnecessary artifacts are avoided in simulations involving polar ...
BACKGROUND In this study, we demonstrated the effects of the Gallic Acid (GA) molecule on the prostate cancer cells line PC3 using the comet assay (Alkaline electrophoresis) technique and its effects on some important apoptotic factors including BAD (Bcl-2-Associated Death promoter), BAK (Bcl-2 homologous Antagonist/Killer), and BIM (Bcl-2-like protein 11) via simulation analysis by using the A...
Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of findi...
Molecular dynamics simulations with coarse-grained and/or simplified Hamiltonians are an effective means of capturing the functionally important long-time and large-length scale motions of proteins and RNAs. Structure-based Hamiltonians, simplified models developed from the energy landscape theory of protein folding, have become a standard tool for investigating biomolecular dynamics. SMOG@ctbp...
MoSGrid is the acronym for Molecular Simulation Grid, a BMBF funded joint research project with the aim to offer grid services for the broad field of molecular simulations in the D-Grid infrastructure. Besides tendering various codes ranging from quantum molecular calculations (e.g. Gaussian, Turbomole) via molecular dynamics (e.g. Gromacs) to docking approaches (e.g. FlexX) for high performanc...
Summary: The do_x3dna package has been developed to analyze the structural fluctuations of DNA or RNA during molecular dynamics simulations. It extends the capability of the 3DNA package to GROMACS MD trajectories and includes new methods to calculate the global-helical axis of DNA and bending fluctuations during simulations. The package also includes a Python module dnaMD to perform and visual...
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