نتایج جستجو برای: gromacs software
تعداد نتایج: 437470 فیلتر نتایج به سال:
In Hard Disk Drives (HDD), it is necessary to decrease the Flying Height (FH) between the head and the disk (currently, FH is around 3-5 nm) so as to increase recording densities. Retaining the solid lubricant has become a difficult proposition owing to intermittent contact between the surfaces. ZTMD and Z are used as solid lubricant to lubricate these interfaces. In this paper, the behavior of...
Introduction: Human Serum Albumin (HSA) is one of the most important proteins in blood that can bind a wide range of components and different drugs such as Warfarin and is also circulated in the body by HSA. Therefore, studying HSA is very significant in pharmacology. In this research, dynamic behavior of residues of Warfain binding site of HSA has been investigated. Methods: Firstly, PDB form...
Introduction: P53 is a tumor suppressor protein with numerous missense mutations identified in its gene. These mutations are observed in a vast number of cancers. R213G is one of them which has a role in metastatic lung cancers. In this research, R213G was studied in comparison with the wild type via molecular dynamics simulation. Method: For the three-dimensional structure of the wild-type P53...
Afzelin has been designed and tested for its in silico antibacterial activity against DNA gyrase complex of Staphyloccocus aureus. The results the toxicity study indicate that afzelin displayed moderate potential staphylococcus aureus with LD50 = 5000 mg/Kg, which is almost four times a half weaker than obtained commercial antibiotic chloramphenicol. chloramphenicol were subjected to docking st...
This study develops a hybrid numerical scheme based on a molecular dynamics (MD) algorithm and the GROMACS protein data bank to analyze the thermal bio-flow of alanine molecules in a microchannel. The numerical results show that the velocity profiles in the microchannel are highly dependent on both global effects, i.e. the effective channel width and local effects, i.e. the thermal boundary con...
ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to calibrate parameters...
A new 3D implementation of a hybrid model based on the analogy with two-phase hydrodynamics has been developed for the simulation of liquids at microscale. The idea of the method is to smoothly combine the atomistic description in the molecular dynamics zone with the Landau-Lifshitz fluctuating hydrodynamics representation in the rest of the system in the framework of macroscopic conservation l...
Breast cancer is the leading cause of cancer-related deaths among women. With clinical success several synthetic aromatase inhibitors (AIs) as therapeutic agents in post-menopausal estrogen receptor-positive breast cancer, natural products have been tapped search chemically diverse compounds with potential better effectiveness against while conferring reduced adverse effects. Alpinia galanga Ph...
The MoSGrid (Molecular Simulation Grid, http://www. mosgrid.de) project aims to provide remote computational chemistry services within the German Grid Initiative (D-Grid). Submission and monitoring of compute jobs, as well as the retrieval of postprocessed results are realized through a web based portal. The use of standardized portlets and a generally modular approach allows for the simultaneo...
Anaphase promoting complex (APC) controls cell cycle and chromosome segregation. The APC activation occurs after binding of co-activators, cdh1 and cdc20. Cdh1 plays a role in cancer pathogenesis and is known as a potential drug target. The main aim of this study was prediction of 3D structure of cdh1 and designing the inhibitory compounds based on the structural model. First, 3D structure of c...
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