<br>Micelle Maker：一种在线工具，用于生成平衡胶束作为分子动力学模拟的直接输入,ACS Omega

当前位置： X-MOL 学术 › ACS Omega › 论文详情

Our official English website, www.x-mol.net, welcomes your feedback! (Note: you will need to create a separate account there.)

Micelle Maker：一种在线工具，用于生成平衡胶束作为分子动力学模拟的直接输入
ACS Omega ( IF 3.7 ) Pub Date : 2017-08-15 00:00:00 , DOI: 10.1021/acsomega.7b00820
Dennis M Krüger ₁ , Shina C L Kamerlin ₁

Affiliation

胶束在脂质相互作用对生物系统影响的实验和计算研究中发挥着重要作用。胶束的球形几何形状和动力学行为使得生成用于分子模拟的胶束结构具有挑战性。非常需要一种简单的工具来生成可用于模拟的胶束模型，涵盖广泛的脂质。在这里，我们提出了一种新的 Web 服务器 Micelle Maker，它可以提供平衡的胶束模型，作为后续各种脂质（目前有 25 种脂质类型，包括 24 种糖脂）分子动力学模拟的直接输入。 Web 服务器可在 http://www.micellemaker.net 上找到，它使用错误检查例程来防止脂质初始放置期间发生冲突，并使用 AMBER 的 GLYCAM 库来生成最小化或平衡的胶束模型，但生成的结构可以可用作任何力场或模拟包的模拟起点。使用提供组装信息的八个胶束模型进行的总体模拟时间为 12 μs 的广泛验证模拟表明，所有胶束在整个模拟时间内都保持非常稳定。最后，我们讨论了 Micelle Maker 相对于该领域其他方法的优势。

"点击查看英文标题和摘要"

Micelle Maker: An Online Tool for Generating Equilibrated Micelles as Direct Input for Molecular Dynamics Simulations

Micelles play an important role in both experimental and computational studies of the effect of lipid interactions on biological systems. The spherical geometry and the dynamical behavior of micelles makes generating micelle structures for use in molecular simulations challenging. An easy tool for generating simulation-ready micelle models, covering a broad range of lipids, is highly desirable. Here, we present a new Web server, Micelle Maker, which can provide equilibrated micelle models as a direct input for subsequent molecular dynamics simulations from a broad range of lipids (currently 25 lipid types, including 24 glycolipids). The Web server, which is available at http://www.micellemaker.net, uses error checking routines to prevent clashes during the initial placement of the lipids and uses AMBER’s GLYCAM library for generating minimized or equilibrated micelle models, but the resulting structures can be used as starting points for simulations with any force field or simulation package. Extensive validation simulations with an overall simulation time of 12 μs using eight micelle models where assembly information is available show that all of the micelles remain very stable over the whole simulation time. Finally, we discuss the advantages of Micelle Maker relative to other approaches in the field.

更新日期：2017-08-15

点击分享查看原文

点击收藏

公开下载

阅读更多本刊最新论文本刊介绍/投稿指南11