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Newman Projections

Newman Projections

Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...

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Updated: Jun 17, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

Published on: March 1, 2022

ezAlign:用于将粗粒度分子动力学结构转换为原子分辨率的工具,用于多尺度建模.

W F Drew Bennett¹, Austen Bernardi¹, Tugba Nur Ozturk¹

¹Lawrence Livermore National Laboratory, Livermore, CA 94550, USA.

Molecules (Basel, Switzerland)

|August 10, 2024

概括

ezAlign软件将粗粒度分子动力学结构转换为原子表示. 这使复杂的生物系统能够进行多尺度建模,弥合不同的时间和长度尺度.

关键词:

分子动力学分子动力学多尺度建模模型的使用.软件软件软件软件软件

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Last Updated: Jun 17, 2025

Structure-Based Simulation and Sampling of Transcription Factor Protein Movements along DNA from Atomic-Scale Stepping to Coarse-Grained Diffusion

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科学领域:

计算物理和化学计算物理和化学
生物分子建模模型
软冷凝物质物理学的物理

背景情况:

研究软凝聚物质和生物分子系统受到巨大的,不同的时间和长度尺度的阻碍.
复杂系统的准确表示需要多尺度的模拟.
弥合这些尺度对于理解生物过程至关重要.

研究的目的:

介绍 ezAlign,一个开源软件,用于将粗粒度分子动力学 (MD) 结构转换为原子表示.
通过使不同模拟尺度的无集成,促进生物分子系统的多尺度建模.
为研究人员提供一个用户友好的工具和全面的例子.

主要方法:

ezAlign采用一种基于将一个原子模板分子对准一个粗粒度结构的方法.
位置-限制能量的最小化用于确保原子分子采用与粗粒度表示一致的形状.
该过程涉及组合,溶解,最小化和平衡分子的位置限制.

主要成果:

在纯的POPC膜上进行了验证,将ezAlign与其他流行的膜构造方法进行了比较.
已成功应用于各种系统,包括表面活性剂自组装,膜蛋白和复杂的细菌和人体血膜模型.
该 ezAlign v1.1 软件包是公开提供与支持的例子和参数文件.

结论:

ezAlign有效地将粗粒度的MD结构转换为原子表示,从而实现多尺度建模.
该软件和提供的资源简化了复杂的生物分子系统的构建,用于模拟.
这项工作有助于未来生物和软物质物理学领域的多尺度建模工作.