AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures

Guillaume Pagès (1) , Sergei Grudinin (1)

1 NANO-D-POST [2018-2020] - Algorithms for Modeling and Simulating Nanosystems [2018-...]

Symmetry is very common among proteins found in structural databases such as the 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 pseudo-symmetry. The method is very fast, as most of the steps are performed analytically.

Mots clés: Protein Symmetry; Protein Assembly; Continuous optimization; Symmetry axes detection; Quaternion arithmetic

Domaines: Bio-informatique [q-bio.QM]; Géométrie algorithmique [cs.CG]; Optimisation et contrôle [math.OC]

Guillaume Pagès, Sergei Grudinin. AnAnaS: Software for Analytical Analysis of Symmetries in Protein Structures. Protein Structure Prediction. Methods in Molecular Biology, pp.245-257, 2020, ⟨10.1007/978-1-0716-0708-4_14⟩. ⟨hal-02931690⟩