Correcting ligands, metabolites, and pathways.
Correcting ligands, metabolites, and pathways.
复制标题
纠正配体，代谢物和途径。
DOI：
10.1186/1471-2105-7-517
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发表时间：
2006-11-28
影响因子：
3
通讯作者：
Vriend G
中科院分区：
文献类型：
--
作者：
Ott MA;Vriend G
生物信息学，分子生物学和药物化学的广泛研究领域需要有关分子和反应的精确化学结构信息，例如药物设计，配体对接，代谢网络重建和系统生物学。但是，大多数可用的数据库将化学结构视为插图，而不是本身就是数据场。缺乏化学精度阻碍了上述领域的进展。我们提出了一个称为Biometa的代谢物数据库，该数据库通过明确评估化学结构和反应信息的有效性，正确性和完整性来增强现有途径数据库。
生物膜中的主要数据是从KEGG配体数据库获得的。我们开发了一种用于化学结构验证的工具，该工具评估了分子描述的化学有效性和立体化学的完整性。验证工具用于检查生物膜中的化合物，表明相对较少的化合物具有不正确的构成（仅连接性，不考虑立体化学），并且相当多的数字（大约三分之一）的立体化学不完全甚至不正确。我们竭尽全力纠正错误并完成结构描述。总共校正了1468个结构和/或完成。我们还建立了生物膜中反应的反应平衡，并在自动过程中纠正了55％的不平衡（静二核法不平衡）反应。 Biometa数据库是在PostgreSQL中实现的，并提供了基于Web的接口。
我们证明了代谢物结构和反应的验证是一项可行且有价值的事业，并且可以使用验证结果来触发对我们代谢物数据库Biometa的校正和改进。 Biometa提供了一些用于理性药物设计，反应搜索和可视化的工具。可以免费提供所有原始数据的版权通知。该数据库将有助于查询和浏览生化途径，并获取用于识别化合物的参考信息。但是，这些应用要求基础数据是正确的，这就是生物疫苗的重点。
A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry) and that a considerable number (about one third) had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect) reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and visualization. It is freely available at provided that the copyright notice of all original data is cited. The database will be useful for querying and browsing biochemical pathways, and to obtain reference information for identifying compounds. However, these applications require that the underlying data be correct, and that is the focus of BioMeta.
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DOI：
10.1021/c160017a018
发表时间：
1965-01-01
期刊：
JOURNAL OF CHEMICAL DOCUMENTATION
影响因子：
--
作者：
MORGAN, HL
通讯作者：
MORGAN, HL
影响因子：
14.9
作者：
Goto, S;Nishioka, T;Kanehisa, M
通讯作者：
Kanehisa, M
DOI：
10.1016/s0166-1280(97)00179-6
发表时间：
1997-12-08
期刊：
THEOCHEM-JOURNAL OF MOLECULAR STRUCTURE
影响因子：
--
作者：
Ertl, P;Jacob, O
通讯作者：
Jacob, O
DOI：
10.1073/pnas.0306458101
发表时间：
2004-02-10
影响因子：
11.1
作者：
Arita, M
通讯作者：
Arita, M
影响因子：
11.4
作者：
Kanehisa, M
通讯作者：
Kanehisa, M