利用PostgreSQL数据库系统探索合作分子接触。

IF 2.8 4区 医学 Q3 CHEMISTRY, MEDICINAL
Mael A Briand, Loïc Dreano, Ashenafi Legehar, Evgeni Grazhdankin, Leo Ghemtio, Henri Xhaard
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引用次数: 0

摘要

协同分子接触在蛋白质结构和配体结合中起着重要作用。在这里,我们构建了一个PostgreSQL数据库,它以原子环境的形式存储结构信息,并允许灵活地挖掘分子接触。以Ser-His-Asp/Glu催化三联体为第一个测试案例,我们证明了在His附近存在羧酸氧原子与较短的Ser-OH相关。PDB30子集中的N-His键。我们前瞻性地挖掘了未注释蛋白中的催化三元组,提示了未注释蛋白的催化功能。作为第二个测试案例,我们通过评估配体羧酸氧的反离子比例,证明该数据库系统可以包括配体原子,以Sybyl原子类型表示。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Exploring cooperative molecular contacts using a PostgreSQL database system.

Exploring cooperative molecular contacts using a PostgreSQL database system.

Cooperative molecular contacts play an important role in protein structure and ligand binding. Here, we constructed a PostgreSQL database that stores structural information in the form of atomic environments and allows flexible mining of molecular contacts. Taking the Ser-His-Asp/Glu catalytic triad as a first test case, we demonstrate that the presence of a carboxylate oxygen atom in the vicinity of a His is associated with shorter Ser-OH..N-His bond in the PDB30 subset. We prospectively mine catalytic triads in unannotated proteins, suggesting catalytic functions for unannotated proteins. As a second test case, we demonstrate that this database system can include ligand atoms, represented by Sybyl atom types, by evaluating the proportion of counter-ions for ligand carboxylate oxygens.

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来源期刊
Molecular Informatics
Molecular Informatics CHEMISTRY, MEDICINAL-MATHEMATICAL & COMPUTATIONAL BIOLOGY
CiteScore
7.30
自引率
2.80%
发文量
70
审稿时长
3 months
期刊介绍: Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010. Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation. The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.
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