ddX:从小分子到蛋白质的可极化连续溶解

IF 16.8 2区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY Wiley Interdisciplinary Reviews: Computational Molecular Science Pub Date : 2024-07-31 DOI:10.1002/wcms.1726
Michele Nottoli, Michael F. Herbst, Aleksandr Mikhalev, Abhinav Jha, Filippo Lipparini, Benjamin Stamm
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引用次数: 0

摘要

可极化连续溶解模型在量子化学和生物物理学中都很流行,但对数值方法的要求通常不同。然而,最近的多尺度建模趋势有望模糊特定领域的差异。在这方面,基于领域分解(dd)的数值方法已被证明具有足够的灵活性,可应用于所有这些理论层面,同时保持系统的准确性和高效性。在这篇论文中,我们介绍了 ddX,它是针对各种溶解模型的 dd 方法的开源实现,具有与溶质的经典和量子描述或其任何混合版本的统一接口。我们解释了库设计的关键概念及其应用程序接口,并演示了如何将 ddX 集成到标准化学软件包中。数值测试说明了 ddX 及其接口的性能:软件 > 量子化学软件 > 模拟方法
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ddX: Polarizable continuum solvation from small molecules to proteins

Polarizable continuum solvation models are popular in both, quantum chemistry and in biophysics, though typically with different requirements for the numerical methods. However, the recent trend of multiscale modeling can be expected to blur field-specific differences. In this regard, numerical methods based on domain decomposition (dd) have been demonstrated to be sufficiently flexible to be applied all across these levels of theory while remaining systematically accurate and efficient. In this contribution, we present ddX, an open-source implementation of dd-methods for various solvation models, which features a uniform interface with classical as well as quantum descriptions of the solute, or any hybrid versions thereof. We explain the key concepts of the library design and its application program interface, and demonstrate the use of ddX for integrating into standard chemistry packages. Numerical tests illustrate the performance of ddX and its interfaces.

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来源期刊
Wiley Interdisciplinary Reviews: Computational Molecular Science
Wiley Interdisciplinary Reviews: Computational Molecular Science CHEMISTRY, MULTIDISCIPLINARY-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
28.90
自引率
1.80%
发文量
52
审稿时长
6-12 weeks
期刊介绍: Computational molecular sciences harness the power of rigorous chemical and physical theories, employing computer-based modeling, specialized hardware, software development, algorithm design, and database management to explore and illuminate every facet of molecular sciences. These interdisciplinary approaches form a bridge between chemistry, biology, and materials sciences, establishing connections with adjacent application-driven fields in both chemistry and biology. WIREs Computational Molecular Science stands as a platform to comprehensively review and spotlight research from these dynamic and interconnected fields.
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