BioSuper

BioSuper performs superimposition of biomolecules and assemblies exhibiting rotational symmetry to enable quantitative comparison of oligomeric protein complexes from the Protein Data Bank (PDB).

Key Features:

• Rotational Symmetry Handling: Accommodates rotational symmetry in protein complexes for accurate superimposition of oligomeric assemblies.
• Root Mean Square Deviation (RMSD): Computes RMSD values for superimposed complexes to quantify structural similarity.
• Biomolecule Generator: Generates biomolecular assemblies within the platform for use in superimposition analyses.
• Atom Selection Flexibility: Supports multiple atom selection levels and both sequence-dependent and structure-based superimposition modes.
• Symmetry Ambiguity Resolution: Considers equivalence of atoms in side chains to resolve symmetry-related atom ambiguities during superimposition.

Scientific Applications:

• Structural alignment of oligomers: Enables precise pairwise alignment and comparison of oligomeric proteins and assemblies with rotational symmetry.
• Analysis of flexible oligomers: Supports analysis of symmetry-related ambiguity and structural divergence in flexible oligomeric complexes.
• Comparative structural analysis using PDB entries: Facilitates quantitative comparison of structures retrieved from the Protein Data Bank (PDB) using RMSD and symmetry-aware superimposition.

Methodology:

BioSuper leverages core functionalities of the ICM (Integrative Computational Modelling) program to perform superimpositions.