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通道数据库：生物大分子隧道和孔数据库。

ChannelsDB: database of biomacromolecular tunnels and pores.

机构信息

CEITEC - Central European Institute of Technology, Masaryk University Brno, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.

National Centre for Biomolecular Research, Faculty of Science, Kamenice 5, 625 00 Brno-Bohunice, Czech Republic.

出版信息

Nucleic Acids Res. 2018 Jan 4;46(D1):D399-D405. doi: 10.1093/nar/gkx868.

DOI:10.1093/nar/gkx868
PMID:29036719
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5753359/
Abstract

ChannelsDB (http://ncbr.muni.cz/ChannelsDB) is a database providing information about the positions, geometry and physicochemical properties of channels (pores and tunnels) found within biomacromolecular structures deposited in the Protein Data Bank. Channels were deposited from two sources; from literature using manual deposition and from a software tool automatically detecting tunnels leading to the enzymatic active sites and selected cofactors, and transmembrane pores. The database stores information about geometrical features (e.g. length and radius profile along a channel) and physicochemical properties involving polarity, hydrophobicity, hydropathy, charge and mutability. The stored data are interlinked with available UniProt annotation data mapping known mutation effects to channel-lining residues. All structures with channels are displayed in a clear interactive manner, further facilitating data manipulation and interpretation. As such, ChannelsDB provides an invaluable resource for research related to deciphering the biological function of biomacromolecular channels.

摘要

ChannelsDB（http://ncbr.muni.cz/ChannelsDB）是一个数据库，提供了在蛋白质数据库中储存的生物大分子结构中发现的通道（孔隙和隧道）的位置、几何形状和物理化学特性的信息。通道来自两个来源：通过文献使用手动沉积和通过一个软件工具自动检测通向酶活性位点和选定辅助因子以及跨膜孔隙的隧道。该数据库存储有关几何特征（例如通道沿线的长度和半径分布）和涉及极性、疏水性、亲水性、电荷和可变性的物理化学特性的信息。存储的数据与可用的 UniProt 注释数据相关联，将已知的突变效应映射到通道衬里残基。所有具有通道的结构都以清晰的交互方式显示，进一步方便了数据的操作和解释。因此，ChannelsDB 为研究生物大分子通道的生物功能提供了宝贵的资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/70ff365fcacf/gkx868fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/86a318ced952/gkx868fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/6868ceec7026/gkx868fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/70ff365fcacf/gkx868fig3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/86a318ced952/gkx868fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/6868ceec7026/gkx868fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/92cb/5753359/70ff365fcacf/gkx868fig3.jpg

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