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Nucleic Acids Res. 2012 Jan;40(Database issue):D472-8. doi: 10.1093/nar/gkr940. Epub 2011 Nov 13.

AH-DB: collecting protein structure pairs before and after binding.

Author information

1
Department of Electrical Engineering, National Cheng Kung University, Tainan 70101, Taiwan. darby@mail.ncku.edu.tw

Abstract

This work presents the Apo-Holo DataBase (AH-DB, http://ahdb.ee.ncku.edu.tw/ and http://ahdb.csbb.ntu.edu.tw/), which provides corresponding pairs of protein structures before and after binding. Conformational transitions are commonly observed in various protein interactions that are involved in important biological functions. For example, copper-zinc superoxide dismutase (SOD1), which destroys free superoxide radicals in the body, undergoes a large conformational transition from an 'open' state (apo structure) to a 'closed' state (holo structure). Many studies have utilized collections of apo-holo structure pairs to investigate the conformational transitions and critical residues. However, the collection process is usually complicated, varies from study to study and produces a small-scale data set. AH-DB is designed to provide an easy and unified way to prepare such data, which is generated by identifying/mapping molecules in different Protein Data Bank (PDB) entries. Conformational transitions are identified based on a refined alignment scheme to overcome the challenge that many structures in the PDB database are only protein fragments and not complete proteins. There are 746,314 apo-holo pairs in AH-DB, which is about 30 times those in the second largest collection of similar data. AH-DB provides sophisticated interfaces for searching apo-holo structure pairs and exploring conformational transitions from apo structures to the corresponding holo structures.

PMID:
22084200
PMCID:
PMC3245139
DOI:
10.1093/nar/gkr940
[Indexed for MEDLINE]
Free PMC Article

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