PocketSCP：一种蛋白质口袋动力学的时空拓扑可视化和分析方法。

IF 5.3 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2025-05-13 DOI:10.1021/acs.jcim.5c00728

Dongliang Guo,Hanqing Zhao,Jiabin Huang,Jiawei Zhao,Ximing Xu,Yapeng Liu,Ying Yang

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引用次数: 0

摘要

口袋的识别和分析对于理解蛋白质的功能机制和治疗潜力至关重要。然而，跟踪这些口袋的动态特性是具有挑战性的。在本文中，我们提出了一种可视化和分析蛋白质口袋动力学的方法，称为PocketSCP。首先，提出了内衬氨基酸原子的表示来表征口袋的时空和拓扑性质。随后，设计了基于参考分子构象的三维映射，生成口袋的三维分布图。为了便于观察和分析，利用蛋白质分子的近球形特性，设计了基于等距方位角投影的三维到二维平面映射。最后，通过实验验证了我们的方法在蛋白质口袋中识别潜在模式的有效性。

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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PocketSCP: A Method for Spatiotemporal Topological Visualization and Analysis of Protein Pocket Dynamics.

The identification and analysis of pockets are crucial for understanding the functional mechanisms and therapeutic potential of proteins. However, it is challenging to track the dynamic characteristics of the pockets. In this paper, we present a method for the visualization and analysis of protein pocket dynamics called PocketSCP. Initially, the representation of lining amino acid atoms is proposed to characterize the spatiotemporal and topological properties of pockets. Subsequently, 3D mapping based on a reference molecular conformation is designed to generate 3D distribution maps of pockets. To facilitate observation and analysis, 3D to 2D plane mapping based on equidistant azimuthal projection is designed, leveraging the near-spherical shape properties of protein molecules. Finally, the efficacy of our method in identifying potential patterns within protein pockets is demonstrated through experimental validation.

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来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.