Symmetry is very common among proteins found in structural databases such as the Protein Data Bank (PDB). We present novel software, called AnAnaS, that finds positions and orientations of the symmetry axes in all types of symmetrical protein assemblies. It deals with five symmetry groups: cyclic, dihedral, tetrahedral, octahedral, and icosahedral. The software also assesses the quality of symmetry and can detect symmetries in incomplete cyclic assemblies. Internally, AnAnaS comprises discrete and continuous optimization steps and is applicable to assemblies with multiple chains in the asymmetric subunits or to those with pseudosymmetry. The method is very fast as most of the steps are performed analytically.
Keywords: Continuous optimization; Protein assembly; Protein symmetry; Quaternion arithmetic; Symmetry axes detection.