AH-DB (Apo and Holo structures DataBase) collects apo and holo structure pairs of proteins.

AH-DB has been updated according to the Protein Data Bank (PDB) release of 27 March 2013. Now AH-DB contains 747036 apo-holo structure pairs of 3683 proteins from 715 organisms. In addition, the statistics page has been re-designed. The new statistics page includes the following informations: number of apo-holo structure pairs by species, number of apo-holo structure pairs by add type, number of apo-holo structure pairs by the type of conformational transitions, number of proteins by species, number of proteins by add type, number of apo-holo structure pairs by root-mean-square deviation (RMSD), number of apo-holo structure pairs by number of added molecules of different type and number of proteins by average root-mean-square deviation (RMSD).
We have offered a new search sample of the heat shock protein of yeast (Hsp90), which is an essential molecular chaperone in eukaryotes. The mutation of four phosphorylation sites (S379, S485, S602 and S604) in Hsp90 have been shown influence on yeast conformational rearrangements..

To see this sample in action, please click the corresponding [Load Sample] button in the AH-DB homepage.
The search options will be loaded to the appropriate fields. After checking the options, click the [Search AH-DB] button to perform the actual search.
After a while, the apo-holo structure pairs that satisfy the search options will be listed on the next page. Clicking the [view] link of a structure pair of your interest to see the details of that pair. This sample chose the fourth pair, which contains the most secondary structure transitions (21).
Please follow the procedure below to highlight the two phosphorylation sites (S379 and S485) that have been shown influence on yeast conformational rearrangements. The other two phosphorylation sites (S602 and S604) are disordered in the selected PDB structures. (a) Uncheck "added molecules" to hide added molecules and to focus on the target protein, Hsp90. (b) Right click on the structure view and then click "console" to open the "Jmol Script Console". (c) Input "select 379, 485" and click [Execute] button to select the 379th and 485th residues of the Hsp90. (d) Now you will see the two phosphorylation sites of Hsp82 in the structure view.
We have made a video to introduce AH-DB.
AH-DB now can save search sessions. It means that users can retrieve their previous search results. In each session, users can see the session ID at the top of AH-DB, as shown in a of the figure below. AH-DB also provides the permanent link of the session (b of the figure below) so that users can bookmakr it for future accesses. The homepage of AH-DB contains a facility for users to input the session ID of retrival. If users forgot to write down the session IDs, the homepage of AH-DB also shows at most five recently assessed sessions IDs.
AH-DB now has its own logo. It contains two arrows, indicating the two directions from apo to holo and vice versa. The blue one indicates the apo state while the red one indicates the holo state. The red arrow is more complicated than the blue one since the holo state is usually more complicated.