Department of Physical Chemistry, Faculty of Science, Palacký University, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.
Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic.
Nucleic Acids Res. 2024 Jan 5;52(D1):D413-D418. doi: 10.1093/nar/gkad1012.
ChannelsDB 2.0 is an updated database providing structural information about the position, geometry and physicochemical properties of protein channels-tunnels and pores-within deposited biomacromolecular structures from PDB and AlphaFoldDB databases. The newly deposited information originated from several sources. Firstly, we included data calculated using a popular CAVER tool to complement the data obtained using original MOLE tool for detection and analysis of protein tunnels and pores. Secondly, we added tunnels starting from cofactors within the AlphaFill database to enlarge the scope of the database to protein models based on Uniprot. This has enlarged available channel annotations ∼4.6 times as of 1 September 2023. The database stores information about geometrical features, e.g. length and radius, and physico-chemical properties based on channel-lining amino acids. The stored data are interlinked with the available UniProt mutation annotation data. ChannelsDB 2.0 provides an excellent resource for deep analysis of the role of biomacromolecular tunnels and pores. The database is available free of charge: https://channelsdb2.biodata.ceitec.cz.
ChannelsDB 2.0 是一个更新的数据库，提供了 PDB 和 AlphaFoldDB 数据库中沉积的生物大分子结构内的蛋白质通道-隧道和孔的位置、几何形状和物理化学性质的结构信息。新沉积的信息来自多个来源。首先，我们包括了使用流行的 CAVER 工具计算的数据，以补充使用原始 MOLE 工具获得的数据，用于检测和分析蛋白质隧道和孔。其次，我们添加了从 AlphaFill 数据库中的辅因子开始的隧道，以扩大数据库的范围，涵盖基于 Uniprot 的蛋白质模型。截至 2023 年 9 月 1 日，这将可用通道注释扩大了约 4.6 倍。该数据库存储了基于通道衬里氨基酸的几何特征（例如长度和半径）和物理化学性质的信息。存储的数据与可用的 UniProt 突变注释数据相互关联。ChannelsDB 2.0 为深入分析生物大分子隧道和孔的作用提供了极好的资源。该数据库免费提供：https://channelsdb2.biodata.ceitec.cz。
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