نتایج جستجو برای: gromacs
تعداد نتایج: 302 فیلتر نتایج به سال:
The 2019 coronavirus pandemic disease (COVID-19) is still declared a global by the World Health Organization (WHO). Therefore, an effort that considered effective in finding therapeutic agents needed to prevent spread of COVID-19 infection. One steps can be chosen utilizing antimicrobial peptides (AMPs) from animal venom targeting specific receptor SARS-CoV-2, namely main protease (Mpro). Throu...
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...
Introduction Intraductal papillary mucinous neoplasms (IPMNs) are a group of exocrine mucin-producing tumors, diagnosed at a mean age of 60 years, with a male prevalence [1]. Improvements in imaging techniques have led to an increasing incidental detection of IPMNs: the prevalence of incidental cystic pancreatic lesions can be observed in up to 19.6% of imaging studies [2]. Three types of IPMNs...
The human transporters for the inhibitory neurotransmitter gamma-aminobutyric acid (GABA) hGAT-1, 2, and 3, and hBGT-1 belong to the neurotransmittersodium symporter (NSS) family of membrane transport proteins. hGAT-1 has been a target for the design of antiepileptic therapeutics [1], with tiagabine (Gabitril) being the only GAT inhibitor on the market. The lack of specific inhibitors for the o...
A new Receptor-Dependent LQTA-QSAR approach, RD-LQTA-QSAR, is proposed as a new 4D-QSAR method. It is an evolution of receptor independent LQTA-QSAR. This approach uses the free GROMACS package to carry out molecular dynamics simulations and generates a conformational ensemble profile for each compound. Such an ensemble is used to build molecular interaction field-based QSAR models, as in CoMFA...
The RIO family [1] of atypical protein kinases are present in organism varying from archea to humans. RIO1 and RIO2 are required for proper ribosome processing in yeast, and for proper cell cycle progression. Deletion of either RIO1 or RIO2 is lethal. Although the biological substrates of RIO kinases are still not known, this family is an important member of the regulation network in a cell. He...
The ion-ion radial distribution functions used in the Iterative Boltzmann Inversion (see main text and the section 2 of this SI Appendix) are calculated from atomistic simulations of NaCl-water solutions. Periodic boundary conditions (PBC) are applied on the x-, yand zdimensions of a 5 nm × 5 nm × 5 nm simulation box. NaCl concentrations from 0.3 M to 1 M are simulated. The number of water mole...
We describe our efforts to prepare common starting structures and models for the SAMPL5 blind prediction challenge. We generated the starting input files and single configuration potential energies for the host-guest in the SAMPL5 blind prediction challenge for the GROMACS, AMBER, LAMMPS, DESMOND and CHARMM molecular simulation programs. All conversions were fully automated from the originally ...
برهم کنش سه ترکیب بازشیف چهار دندانه 1و3-بیس(2-هیدروکسی–بنزآلیدین)–اوره و مشتقات دی متوکسی و کمپلکس نیکل آن با dna طحال گوساله (ct-dna) به وسیله ی روش های طیف سنجی uv-vis، فلوئورسانس، دورنگ نمایی دورانی، ویسکوزیته، ولتامتری چرخه ای، تکنیک دمای گذار، شبیه سازی داکینگ مولکولی و شبیه سازی دینامیک مولکولی مورد بررسی قرار گرفت. نتایج بدست آمده از روش های فوق حاکی از وجود برهم کنش اینترکلیشن در سیستم...
Background & Aims: The normal form of the prion protein is called PrPC and its infectious form is called PrPSc. This protein functions like a crystallized core for the transformation of PrPc into an abnormal PrPSc. The aim of the present study was to investigate the effect of temperature on human prion protein structure through molecular dynamic simulation. Methods: In this research, the GROMAC...
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