PDB-2-PBv3.0: An updated protein block database.

Muthuvel Prasath Karuppasamy, Suresh Venkateswaran, Parthasarathy Subbiah

Journal of bioinformatics and computational biology 2020 Apr

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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.

Citation

Muthuvel Prasath Karuppasamy, Suresh Venkateswaran, Parthasarathy Subbiah. PDB-2-PBv3.0: An updated protein block database. Journal of bioinformatics and computational biology. 2020 Apr;18(2):2050009