gorder:从分子模拟中计算脂质顺序参数的综合工具

IF 2.4 4区 计算机科学 Q2 COMPUTER SCIENCE, SOFTWARE ENGINEERING
Ladislav Bartoš , Peter Pajtinka , Robert Vácha
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引用次数: 0

摘要

脂质序参数是定量生物膜分子结构的重要指标。它们可以从分子模拟和实验测量中得到,从而实现两者之间的可靠比较。尽管从不同分辨率的膜系统分子动力学模拟中计算脂质顺序参数的方法已经很好地建立起来,但缺乏一个全面和用户友好的计算包,这甚至导致一些研究人员使用已知的工具来错误地执行计算。为了解决这个问题,我们开发了gorder,这是一种分析工具,能够计算原子、联合原子和粗粒度系统中的脂质有序参数,兼容任何力场,适用于平面和弯曲膜几何。Gorder的设计是快速和通用的,为脂质顺序计算提供了统一的解决方案。该工具在MIT许可下可从https://crates.io/crates/gorder和https://github.com/Ladme/gorder免费获得。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
gorder: Comprehensive tool for calculating lipid order parameters from molecular simulations
Lipid order parameters are an important metric for quantifying the molecular structure of biological membranes. They can be derived from both molecular simulations and experimental measurements, enabling robust comparisons between the two. Although methods for calculating lipid order parameters from molecular dynamics simulations of membrane systems at various resolutions are well established, a comprehensive and user-friendly package for these calculations is lacking, which has even led some researchers to use tools that are known to perform the calculations incorrectly. To address this, we have developed gorder, an analysis tool capable of calculating lipid order parameters in atomistic, united-atom, and coarse-grained systems, compatible with any force field, and applicable to both planar and curved membrane geometries. gorder is designed to be fast and versatile, providing a unified solution for lipid order calculations. The tool is freely available from https://crates.io/crates/gorder and https://github.com/Ladme/gorder under the MIT License.
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来源期刊
SoftwareX
SoftwareX COMPUTER SCIENCE, SOFTWARE ENGINEERING-
CiteScore
5.50
自引率
2.90%
发文量
184
审稿时长
9 weeks
期刊介绍: SoftwareX aims to acknowledge the impact of software on today''s research practice, and on new scientific discoveries in almost all research domains. SoftwareX also aims to stress the importance of the software developers who are, in part, responsible for this impact. To this end, SoftwareX aims to support publication of research software in such a way that: The software is given a stamp of scientific relevance, and provided with a peer-reviewed recognition of scientific impact; The software developers are given the credits they deserve; The software is citable, allowing traditional metrics of scientific excellence to apply; The academic career paths of software developers are supported rather than hindered; The software is publicly available for inspection, validation, and re-use. Above all, SoftwareX aims to inform researchers about software applications, tools and libraries with a (proven) potential to impact the process of scientific discovery in various domains. The journal is multidisciplinary and accepts submissions from within and across subject domains such as those represented within the broad thematic areas below: Mathematical and Physical Sciences; Environmental Sciences; Medical and Biological Sciences; Humanities, Arts and Social Sciences. Originating from these broad thematic areas, the journal also welcomes submissions of software that works in cross cutting thematic areas, such as citizen science, cybersecurity, digital economy, energy, global resource stewardship, health and wellbeing, etcetera. SoftwareX specifically aims to accept submissions representing domain-independent software that may impact more than one research domain.
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