03. Membrane Builder - Quick Bilayer Using MolCube LNPDB скачать в хорошем качестве

03. Membrane Builder - Quick Bilayer Using MolCube LNPDB

Here is the Quick Bilayer using MolCube LNPDB tutorial. Join MolCube apps to expand your research horizons! Try it : https://apps.molcube.com/ For more information : https://apps.molcube.com/help/getting... Script : Today, I will demonstrate how to use the Quick Bilayer module, one of the Quick Builder tools provided by MolCube, to build an atomistic bilayer system for lipid nanoparticles, or LNP. To create an LNP bilayer system, we first need formulation information, specifically, the composition and the molar ratios of its components. This information can be obtained from the LNPDB. LNPDB is the first curated web database dedicated to LNP formulations, consolidating sparse and scattered information into one unified platform. It currently contains around 17,000 formulations and about 10,000 unique ionizable lipids collected from 29 publications. It provides access to ionizable lipid libraries, formulations, experimental methods and values, and also CHARMM force field parameters for molecular simulations. The database is continuously updated with the latest datasets, and users can also upload their own datasets. Now let’s fetch a bilayer formulation. From the top menu, click on Search, then choose Search by Properties. A filterable table will appear on the left sidebar. Here, we’ll select Broadpharm under the Library code. This brings up all formulations from the Broadpharm dataset. If you click on a specific LNP ID, we can see the representative ionizable lipid’s 2D and 3D structures, along with downloadable CHARMM force field parameters. Returning to the table, we can hover over the composition field to quickly preview the structures. For this demo, let’s use the LNP formulation with the ionizable lipid BP-25498. On the far right side of the table, click the MolCube icon labeled Copy to clipboard. This copies the full formulation information. Next, we switch to the Quick Bilayer module. Here, we choose Membrane Only because the goal here is to model an isolated bilayer patch of the LNP, without additional solutes or macromolecules. Select Membrane Only, and enter the project title as BP-25498. In the Lipid Selection field, simply paste the information copied from the LNPDB. The exact formulation data from the database is now loaded automatically. If you’d like to build a different type of bilayer or membrane, you can click the question-mark help icon to learn more about text-based lipid input. After that, click Apply, enter the required simulation details, choose your preferred MD engine, and then click Submit. Within moments, the bilayer system will be generated. Finally, this newly built system is fully compatible with MolCube Simulator and MolCube Analyzer, enabling seamless execution of simulations and analysis in one integrated workflow.