نتایج جستجو برای: gromacs
تعداد نتایج: 302 فیلتر نتایج به سال:
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...
We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa-Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation o...
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...
Machine Learning-assisted Lipid Phase Analysis (MLLPA) is a new Python 3 module developed to analyze phase domains in lipid membrane based on molecular states. Reading standard simulation coordinate and trajectory files, the software first composition of by using machine learning tools label each individual molecules with respect their state, then decompose box Voronoi tessellations local envir...
This work aims to explore theoretically the molecular mechanisms of ligand binding to proteins through the use of molecular dynamics simulations. The binding of sodium dodecyl sulfate (SDS) to cobra cardio toxin A3 (CTX A3) and thiourea (TOU) to lysozyme have been chosen as the two model systems. Data acquisitions were made by Gromacs software. To begin with, the collisions of ligand molecules ...
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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