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 users for Linux (64 and 32bit) as well as Mac and Windows as part of our NAOMI ChemBio Suite. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run ASCONA. All feedback is hightly appreciated.
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.