利用 CABS-flex 建模从结构灵活性中探索蛋白质功能。

IF 4.5 3区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Protein Science Pub Date : 2024-09-01 DOI:10.1002/pro.5090
Chandran Nithin, Rocco Peter Fornari, Smita P Pilla, Karol Wroblewski, Mateusz Zalewski, Rafał Madaj, Andrzej Kolinski, Joanna M Macnar, Sebastian Kmiecik
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引用次数: 0

摘要

要了解蛋白质的功能,往往需要确定蛋白质结构的灵活性。然而,由于蛋白质系统具有复杂的动力学特性,模拟蛋白质的柔韧性面临着巨大的挑战,需要大量的计算资源和精确的建模技术。为了应对这些挑战,我们开发了 CABS-flex 方法,它是一种高效的建模工具,将粗粒度模拟与全原子细节相结合。CABS-flex 既有网络服务器版,也有独立软件包版,面向广大用户。网络服务器版为直接任务提供了一个易于使用的界面,而单机版命令行程序则专为高级用户设计,提供了更多的功能、分析工具和处理大型系统的支持。本文探讨了 CABS-flex 在各种结构-功能研究中的应用,促进了不同研究领域对蛋白质结构、动力学和功能之间相互作用的研究。我们概述了 CABS-flex 方法的现状,重点介绍了其最新进展、实际应用和即将面临的挑战。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Exploring protein functions from structural flexibility using CABS-flex modeling.

Understanding protein function often necessitates characterizing the flexibility of protein structures. However, simulating protein flexibility poses significant challenges due to the complex dynamics of protein systems, requiring extensive computational resources and accurate modeling techniques. In response to these challenges, the CABS-flex method has been developed as an efficient modeling tool that combines coarse-grained simulations with all-atom detail. Available both as a web server and a standalone package, CABS-flex is dedicated to a wide range of users. The web server version offers an accessible interface for straightforward tasks, while the standalone command-line program is designed for advanced users, providing additional features, analytical tools, and support for handling large systems. This paper examines the application of CABS-flex across various structure-function studies, facilitating investigations into the interplay among protein structure, dynamics, and function in diverse research fields. We present an overview of the current status of the CABS-flex methodology, highlighting its recent advancements, practical applications, and forthcoming challenges.

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来源期刊
Protein Science
Protein Science 生物-生化与分子生物学
CiteScore
12.40
自引率
1.20%
发文量
246
审稿时长
1 months
期刊介绍: Protein Science, the flagship journal of The Protein Society, is a publication that focuses on advancing fundamental knowledge in the field of protein molecules. The journal welcomes original reports and review articles that contribute to our understanding of protein function, structure, folding, design, and evolution. Additionally, Protein Science encourages papers that explore the applications of protein science in various areas such as therapeutics, protein-based biomaterials, bionanotechnology, synthetic biology, and bioelectronics. The journal accepts manuscript submissions in any suitable format for review, with the requirement of converting the manuscript to journal-style format only upon acceptance for publication. Protein Science is indexed and abstracted in numerous databases, including the Agricultural & Environmental Science Database (ProQuest), Biological Science Database (ProQuest), CAS: Chemical Abstracts Service (ACS), Embase (Elsevier), Health & Medical Collection (ProQuest), Health Research Premium Collection (ProQuest), Materials Science & Engineering Database (ProQuest), MEDLINE/PubMed (NLM), Natural Science Collection (ProQuest), and SciTech Premium Collection (ProQuest).
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