SymmDock

SymmDock predicts structures of cyclically symmetric protein complexes using geometry-based molecular docking to infer homomultimer arrangements from monomeric units.

Key Features:

• Cyclic Symmetry Prediction: Predicts structures of protein complexes exhibiting cyclic symmetry to model arrangements of identical subunits.
• Geometry-Based Molecular Docking: Uses an efficient geometry-based docking approach to generate symmetric assemblies.
• Monomer-to-Homomultimer Assembly: Given a monomeric unit, predicts the arrangement and interactions of identical subunits in the complex.
• Protein Data Bank (PDB) Support: Accepts Protein Data Bank (PDB) structures as input for docking and assembly prediction.
• Integration with BioInfo3D and PatchDock: Interoperates with the BioInfo3D suite and PatchDock for complementary protein–protein and protein–small molecule interaction analyses.
• No Flexible-Region Specification Required: Operates without prior knowledge or specification of flexible regions within the proteins.

Scientific Applications:

• Protein-Protein Interactions: Facilitates characterization of interfaces and assembly modes in multimeric proteins.
• Structural Biology Research: Supports large-scale docking experiments to explore multimeric assembly hypotheses and structural models.

Methodology:

SymmDock employs an efficient geometry-based molecular docking approach; given the structure of a monomeric unit, it predicts the arrangement and interaction of identical subunits in a cyclically symmetric complex and does not require prior specification of flexible regions.