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

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 increas...

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Vydáno v:Journal of bioinformatics and computational biology Ročník 18; číslo 2; s. 2050009
Hlavní autoři: Karuppasamy, Muthuvel Prasath, Venkateswaran, Suresh, Subbiah, Parthasarathy
Médium: Journal Article
Jazyk:angličtina
Vydáno: Singapore 01.04.2020
Témata:
protein data bank
Protein blocks
protein molecular functions
local protein structures
ISSN:1757-6334, 1757-6334
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Shrnutí: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.
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ISSN:1757-6334
1757-6334
DOI:10.1142/S0219720020500092