IPAMD: A Plugin-Based Software for Biomolecular Condensate Simulations.

IF 5.7 1区化学 Q2 CHEMISTRY, PHYSICAL

Journal of Chemical Theory and Computation Pub Date : 2025-05-27 DOI:10.1021/acs.jctc.5c00147

Xiao-Yang Liu,You-Liang Zhu,Yu-Ze Jiang,Shao-Kang Shi,Li Zhao,Zhong-Yuan Lu

引用次数: 0

Abstract

The study of intrinsically disordered proteins (IDPs) and their role in biomolecular condensate formation has become a critical area of research, offering insights into fundamental biological processes and therapeutic development. Here, we present IPAMD (Intrinsically disordered Protein Aggregation Molecular Dynamics), a plugin-based software designed to simulate the formation dynamics of biomolecular condensates of IDPs. IPAMD provides a modular, efficient, and customizable simulation platform specifically designed for biomolecular condensate studies. It incorporates advanced force fields, such as HPS-based and Mpipi models, and employs optimization techniques for large-scale simulations. The software features a user-friendly interface and supports batch processing, making it accessible to researchers with varying computational expertise. Benchmarking and case studies demonstrate the ability of IPAMD to accurately simulate and analyze condensate structures and properties.

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IPAMD：基于插件的生物分子凝聚模拟软件。

内在无序蛋白（IDPs）及其在生物分子凝聚形成中的作用的研究已成为一个关键的研究领域，为基础生物学过程和治疗开发提供了见解。在这里，我们提出了IPAMD（内在无序蛋白质聚集分子动力学），一个基于插件的软件，旨在模拟IDPs生物分子凝聚物的形成动力学。IPAMD提供了一个模块化的、高效的、可定制的模拟平台，专门为生物分子冷凝水研究而设计。它结合了先进的力场，如基于hps和Mpipi模型，并采用优化技术进行大规模模拟。该软件具有用户友好的界面，并支持批处理，使其可访问的研究人员与不同的计算专业知识。基准测试和案例研究表明，IPAMD能够准确地模拟和分析凝析油的结构和性质。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of Chemical Theory and Computation 化学-物理：原子、分子和化学物理

CiteScore

9.90

自引率

16.40%

发文量

568

审稿时长

1 months

期刊介绍： The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.