Conformational transitions are commonly observed in various protein interactions which carry out important biological functions. For example, adenylate
kinase (AdK), which catalyzes the phosphoryl transfer from ATP to AMP, undergoes a large conformational variation from an open state (the apo structure) to a
closed state (the holo structure).
Other examples such as proteins responsible for gene regulation, signal transduction and ion flow also have notable
conformational transitions. There have been many studies analyzing a collection of apo and holo structure pairs to investigate the conformational transitions
and/or critical residues in protein-protein, -nucleic acid and -ligand interactions.
However, most of these studies compiled the apo-holo pairs from scratch.
The collection process was usually complicated, varied from article to article and produced a small-scale dataset (less than 1000 pairs).
This study presents AH-DB, Apo and Holo structure DataBase, which provides an easy and unified way to prepare apo-holo pairs for proteins of interests.
It contains 572,921 apo-holo pairs of 3,377 proteins from 681 organisms.
AH-DB categorized molecules into proteins, nucleic acids, ligands and ions and identified/mapped molecules among complex structures from different Protein Data Bank (PDB) entries to pair apo and holo structures.
AH-DB (Apo and Holo structures DataBase) collects the apo and holo structure pairs of proteins. Proteins are frequently associated with other molecules to perform their functions. Experimental structures determined in the bound state are named holo structures; while structures determined in the unbound state are named apo structures.
In AH-DB, we extended the definition of apo and holo structures. The apo strcuture of a protein could be in a apo complex containing other molecules. The corresponding holo strcuture must be in a holo complex containing all molecules in the apo complex and some added molecules.
AH-DB is the largest database focusing on pairing apo and holo strctures and provide a sophisticated view of the paired structures. It collects 562424 apo-holo pairs, covering 3369 proteins from 677 organisms. See more detailed statistics.
AH-DB pairs protein structures before and after binding.
Some conventions, e.g. the structure before binding is called "apo" structure, are widely used in this area.
Here we clarify the terminology used in AH-DB.
The default list of ligands that are not substrates or natural ligands, namely these compounds are not considered as added molecules by default, in AH-DB.
In AH-DB, the set of residue pairs in an apo-holo structure pair are regarded as a set of paired vectors in the 3D vector space, where a residue is represented by its alpha carbon.
Two superimposition algorithms were adopted to generate the superimposition of the apo and holo structures of a target protein according to the residue mapping obtained in the previous steps.
The following figure shows the home page of AH-DB, which provides a search facility for users to browse AH-DB.
The search facility includes four major parts:
The following figure shows the search result page of AH-DB, which lists all pairs that satisfy the search settings.
This page includes two areas:
The following figure shows the pair page of AH-DB, which shows details of an apo and holo structure pair.
This page consists of four areas:
AH-DB provides a sophisticated keyword search for users to specify target proteins and added molecules of interest.
To wrap it up, "ID OR DESC1 DESC2 AND DESC3* - DESC4" searches molecules satisfying either i) with ID or ii) with "DESC1 DESC2" and DESC3 but without DESC4.
Note the precedence of OR and the concatenation of DESC1 and DESC2.
For better experience, AH-DB utilized many modern web technologies such as AJAX.
We provide some checkpoints to help people who have no idea about these web technologies.
It would be very nice if you can tell us your environment in which AH-DB runs well.
On the other hand, please feel free to contact us when you cannot use AH-DB on a specific environment.
We will test AH-DB on your environment as soon as possible.
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