PDB-2-PBv3.0: An updated protein block database
PDB-2-PBv3.0: An updated protein block database
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DOI：
10.1142/s0219720020500092
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发表时间：
2020-04-01
影响因子：
1
通讯作者：
Subbiah, Parthasarathy
中科院分区：
文献类型：
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作者：
Karuppasamy, Muthuvel Prasath;Venkateswaran, Suresh;Subbiah, Parthasarathy
我们的蛋白质块（PB）序列数据库PDB-2-PBv1.0提供了74，297个蛋白质结构的PB序列和二面角，这些蛋白质结构包括2011年蛋白质数据库（PDB）的103，252条蛋白质链。由于PB的实际应用很多，并且随着PDB数据库的大小增加，提供所有PDB蛋白质结构的PB序列变得必要。当前更新的PDB-2-PBv3.0包含截至2019年10月的147，602个PDB结构的PB序列，包括400，355条蛋白质链。与我们以前的版本PDB-2-PBv1.0相比，当前的PDB-2-PBv3.0包含的蛋白质结构和链的数量分别增加了2倍和4倍。值得注意的是，它为任何蛋白质链提供PB信息，无论PDB中蛋白质结构数据的原子记录是否缺失。它包括蛋白质与DNA和RNA的相互作用信息沿着来自核酸数据库（NDB）和PDB的相应功能类别。现在，更新后的版本允许用户通过参数搜索和/或给定列表下载多个PB记录。该数据库可在http://bioinfo.bdu.ac.in/pb3上免费访问。
Our protein block (PB) sequence database PDB-2-PBv1.0 provides PB sequences and dihedral angles for 74,297 protein structures comprising of 103,252 protein chains of Protein Data Bank (PDB) as on 2011. Since there are a lot of practical applications of PB and also as the size of PDB database increases, it becomes necessary to provide the PB sequences for all PDB protein structures. The current updated PDB-2-PBv3.0 contains PB sequences for 147,602 PDB structures comprising of 400,355 protein chains as on October 2019. When compared to our previous version PDB-2-PBv1.0, the current PDB-2-PBv3.0 contains 2- and 4-fold increase in the number of protein structures and chains, respectively. Notably, it provides PB information for any protein chain, regardless of the missing atom records of protein structure data in PDB. It includes protein interaction information with DNA and RNA along with their corresponding functional classes from Nucleic Acid Database (NDB) and PDB. Now, the updated version allows the user to download multiple PB records by parameter search and/or by a given list. This database is freely accessible at http://bioinfo.bdu.ac.in/pb3.