Wrapping Up Viruses at Multiscale Resolution: Optimizing PACKMOL and SIRAH Execution for Simulating the Zika Virus was written by Sonora, Martin;Martinez, Leandro;Pantano, Sergio;Machado, Matias R.. And the article was included in Journal of Chemical Information and Modeling in 2021.Product Details of 26662-94-2 The following contents are mentioned in the article:
Simulating huge biomol. complexes of million atoms at relevant biol. time scales is becoming accessible to the broad scientific community. That proves to be crucial for urgent responses against emergent diseases in real time. Yet, there are still issues to sort regarding the system setup so that mol. dynamics (MD) simulations can be run in a simple and standard way. Here, we introduce an optimized pipeline for building and simulating enveloped virus-like particles (VLP). First, the membrane packing problem is tackled with new features and optimized options in PACKMOL. This allows preparing accurate membrane models of thousands of lipids in the context of a VLP within a few hours using a single CPU. Then, the assembly of the VLP system is done within the multiscale framework of the coarse-grained SIRAH force field. Finally, the equilibration protocol provides a system ready for production MD simulations within a few days on broadly accessible GPU resources. The pipeline is applied to study the Zika virus as a test case for large biomol. systems. The VLP stabilizes at approx. 0.5渭s of MD simulation, reproducing correlations greater than 0.90 against exptl. d. maps from cryo-electron microscopy. Detailed structural anal. of the protein envelope also shows very good agreement in root-mean-square deviations and B-factors with the exptl. data. The level of details attained shows for the first time a possible role for anionic phospholipids in stabilizing the envelope. Combining an efficient and reliable setup procedure with an accurate coarse-grained force field provides a valuable pipeline for simulating arbitrary viral systems or subcellular compartments, paving the way toward whole-cell simulations. This study involved multiple reactions and reactants, such as (2R,9Z)-1-(((2-Aminoethoxy)(hydroxy)phosphoryl)oxy)-3-(palmitoyloxy)propan-2-yl oleate (cas: 26662-94-2Product Details of 26662-94-2).
(2R,9Z)-1-(((2-Aminoethoxy)(hydroxy)phosphoryl)oxy)-3-(palmitoyloxy)propan-2-yl oleate (cas: 26662-94-2) belongs to esters. Esters are widespread in nature and are widely used in industry. In nature, fats are in general triesters derived from glycerol and fatty acids. Esters are responsible for the aroma of many fruits, including apples, durians, pears, bananas, pineapples, and strawberries. Acyl chlorides and acid anhydrides alcoholysis is another way to produce esters. Acyl chlorides and acid anhydrides react with alcohols to produce esters. Anydrous conditions are recommended since both acyl chlorides and acid anhydrides react with water.Product Details of 26662-94-2
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Ester – an overview | ScienceDirect Topics