Q-BioLiP: A Comprehensive Resource for Quaternary Structure-based Protein–ligand Interactions

IF 11.5 2区生物学 Q1 GENETICS & HEREDITY

Genomics, Proteomics & Bioinformatics Pub Date : 2024-01-04 DOI:10.1093/gpbjnl/qzae001

Hong Wei, Wenkai Wang, Zhenling Peng, Jianyi Yang

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Abstract Since its establishment in 2013, BioLiP has become one of the widely used resources for protein–ligand interactions. Nevertheless, several known issues occurred with it over the past decade. For example, the protein–ligand interactions are represented in the form of single-chain-based tertiary structures, which may be inappropriate as many interactions involve multiple protein chains (known as quaternary structures). We sought to address these issues, resulting in Q-BioLiP, a comprehensive resource for quaternary structure-based protein–ligand interactions. The major features of Q-BioLiP include: (1) representing protein structures in the form of quaternary structures rather than single-chain-based tertiary structures; (2) pairing DNA/RNA chains properly rather than separation; (3) providing both experimental and predicted binding affinities; (4) retaining both biologically relevant and irrelevant interactions to alleviate the problem of the wrong justification of ligands’ biological relevance; and (5) developing a new quaternary structure-based algorithm for the modelling of protein–ligand complex structure. With these new features, Q-BioLiP is expected to be a valuable resource for studying biomolecule interactions, including protein–small molecule interaction, protein–metal ion interaction, protein–peptide interaction, protein–protein interaction, protein–DNA/RNA interaction, and RNA–small molecule interaction. Q-BioLiP is freely available at https://yanglab.qd.sdu.edu.cn/Q-BioLiP/.

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Q-BioLiP：基于四元结构的蛋白质配体相互作用综合资源库

摘要自 2013 年建立以来，BioLiP 已成为广泛使用的蛋白质配体相互作用资源之一。然而，在过去十年中，它也出现了一些已知的问题。例如，蛋白质-配体相互作用以基于单链的三级结构形式表示，这可能并不合适，因为许多相互作用涉及多个蛋白质链（称为四级结构）。为了解决这些问题，我们开发了 Q-BioLiP，这是一种基于四元结构的蛋白质配体相互作用综合资源。Q-BioLiP 的主要特点包括(1) 以四元结构而非基于单链的三级结构的形式表示蛋白质结构；(2) 正确配对 DNA/RNA 链而非分离；(3) 同时提供实验结合亲和力和预测结合亲和力；(4) 保留生物相关和不相关的相互作用，以减轻配体生物相关性的错误论证问题；以及 (5) 开发基于四元结构的新算法，用于蛋白质-配体复合物结构建模。有了这些新功能，Q-BioLiP 将成为研究生物大分子相互作用（包括蛋白质-小分子相互作用、蛋白质-金属离子相互作用、蛋白质-肽相互作用、蛋白质-蛋白质相互作用、蛋白质-DNA/RNA 相互作用以及 RNA-小分子相互作用）的宝贵资源。Q-BioLiP 可在 https://yanglab.qd.sdu.edu.cn/Q-BioLiP/ 免费获取。

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

Genomics, Proteomics & Bioinformatics Biochemistry, Genetics and Molecular Biology-Biochemistry

CiteScore

14.30

自引率

4.20%

发文量

844

审稿时长

61 days

期刊介绍： Genomics, Proteomics and Bioinformatics (GPB) is the official journal of the Beijing Institute of Genomics, Chinese Academy of Sciences / China National Center for Bioinformation and Genetics Society of China. It aims to disseminate new developments in the field of omics and bioinformatics, publish high-quality discoveries quickly, and promote open access and online publication. GPB welcomes submissions in all areas of life science, biology, and biomedicine, with a focus on large data acquisition, analysis, and curation. Manuscripts covering omics and related bioinformatics topics are particularly encouraged. GPB is indexed/abstracted by PubMed/MEDLINE, PubMed Central, Scopus, BIOSIS Previews, Chemical Abstracts, CSCD, among others.