ProCogGraph: a graph-based mapping of cognate ligand domain interactions.

IF 2.4 Q2 MATHEMATICAL & COMPUTATIONAL BIOLOGY

Bioinformatics advances Pub Date : 2024-10-22 eCollection Date: 2024-01-01 DOI:10.1093/bioadv/vbae161

Matthew Crown, Matthew Bashton

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引用次数: 0

Abstract

Motivation: Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts.

Results: We present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we use the graph to add specificity to partial EC IDs, showing that ProCogGraph can complete partial annotations systematically through assigned cognate ligands.

Availability and implementation: The ProCogGraph pipeline, database and flat files are available at https://github.com/bashton-lab/ProCogGraph and https://doi.org/10.5281/zenodo.13165851.

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ProCogGraph：基于图形的同源配体结构域相互作用图谱。

动机：结构域与认知配体相互作用的映射可以加深我们对进化核心概念的理解，并用于辅助对接和蛋白质设计。自从上一次发布认知配体结构域数据库以来，PDB 已经有了长足的发展，并且有了测量相似性和确定接触的新工具：我们介绍了 ProCogGraph，这是一个 PDB 结构中认知配体结构域映射的图数据库。在前身数据库 PROCOGNATE 的基础上，我们使用数据驱动方法来开发阈值和相互作用模式。我们探索了结构域与同源配体相互作用的新方面，包括结合的同源配体的化学相似性以及结构域组合如何影响同源配体的结合。最后，我们利用图谱为部分 EC ID 添加特异性，表明 ProCogGraph 可以通过指定的同源配体系统地完成部分注释：ProCogGraph 管道、数据库和平面文件可在 https://github.com/bashton-lab/ProCogGraph 和 https://doi.org/10.5281/zenodo.13165851 上获取。

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来源期刊

Bioinformatics advances

CiteScore

1.60

自引率

0.00%

发文量