University of Hamburg - to research, to teach, to educate and form, to homepage
ZBH
ZBHCenter for Bioinformatics

Photo: UHH/Denstorf

ASCONA

Overview

ASCONA is a fully automated command-line tool for generating sequence alignments and superpositions of protein binding sites. It is geared 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 can also deal with point mutations. Given its high reliability and efficient performance, ASCONA is perfectly suited for preprocessing protein structure ensembles used to model 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 to a target structure
  3. binding site reconstruction with a geometry-based assembly approach


Software Availability

ASCONA is freely available for non-commercial and academic users for Linux, MacOS, and Windows as part of our NAOMI ChemBio Suite. To download ASCONA, register at https://software.zbh.uni-hamburg.de. Non-academic users can get an evaluation license free of charge. Only minimal setup steps are required to run ASCONA. All feedback (software.zbh(at)uni-hamburg.de) is highly appreciated.

References

Bietz, S.; Rarey, M. ASCONA: Rapid Detection and Alignment of Protein Binding Site Conformations. J Chem Inf Model 2015, 55 (8), 1747-1756. DOI: https://doi.org/10.1021/acs.jcim.5b00210