ASCONA is a fully automated command line tool for generating sequence alignments and superpositions of protein binding sites. Itisgeared to the alignment of alternative protein conformations and especially addresses the tasks of
- dealing with highly flexible backbone regions,
- detecting multiple occurrences of a binding site in oligomeric structures, and
- coping with arbitrary annotation inconsistencies and structural artifacts.
Moreover, ASCONA is also able to deal with point mutations. Given its high reliability and efficient performance, ASCONA is a perfectly suited tool for preprocessing protein structure ensembles that shall be used for modeling protein flexibility.
ASCONA uses a fragment based search strategy that consists of the following steps:
- Fragmentation of a given active site definition into short peptide fragments
- Sequence alignment of all query fragments against a target structure
- Binding site reconstruction with a geometry based assembly approach.
ASCONA is freely available for academic use for Linux. Non-academic users can get an evaluation licence free of charge. Only minimal setup steps are required to run ASCONA. All feedback (ascona(at)zbh.uni-hamburg.de) is highly appreciated.
ASCONA is part of the AMD tools software bundle. To download ASCONA, register at
People and references
 Bietz, S. Rarey, M.: ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. Journal of Chemical Information and Modeling, 55(8):1747–1756.