ASCONA

Overview

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

1. dealing with highly flexible backbone regions,
2. detecting multiple occurrences of a binding site in oligomeric structures, and 
3. 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.

Method

ASCONA uses a fragment based search strategy that consists of the following steps:

1. Fragmentation of a given active site definition into short peptide fragments
2. Sequence alignment of all query fragments against a target structure
3. Binding site reconstruction with a geometry based assembly approach.

Software Availability

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
https://software.zbh.uni-hamburg.de.

People and references

[1] Bietz, S. Rarey, M.: ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. Journal of Chemical Information and Modeling, 55(8):1747–1756.