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.