Galaxy | Tool Preview

APoc (version 1.0+galaxy1)
Alignment options
Alignment option 0
Scoring options
Scoring option 0


APoc may be used to compare two pockets, a pocket against a set of pockets, or all-against-all between two sets of pockets. If you supply two structures to compare, the first structure is the template and the second structure is the query (or target).

For each pair of structures, the program first performs a global structural comparison in sequential order using a standard TM-align algoritm. One may elect to bypass the global alignment to accelerate comparison. If no pocket found in the pdb structures, the program becomes a normal TM-align or stop if one chooses to bypass the global alignment. If there are pockets detected in the input files, it will compare pockets in sequential-order-independent manner by default.

The ouput is arranged in pairs of structures compared. For each pair, the first alignment is the global alignment, followed by all-againat-all alignment of selected pockets. If you want a concise output without detailed alignment, add the "-v 0" option.