GalaxyHomomer

GalaxyHomomer predicts three-dimensional structures of protein homo-oligomers to determine subunit assembly and support studies of molecular function and regulation.

Key Features:

• Template-Based Modeling: Uses templates from protein structure databases to model oligomer arrangements when suitable homologous oligomer structures exist.
• Ab Initio Docking: Performs ab initio docking of monomers using their resolved or predicted structures to explore oligomer configurations when templates are absent.
• Hybrid Approach: Combines template-based modeling and ab initio docking depending on available data to broaden prediction coverage.
• Model Refinement: Applies model refinement methods to improve structural accuracy and conformational consistency with biophysical principles.
• Customizable Options: Allows specification of monomer structure, oligomeric state, and regions such as unreliable or flexible loops and termini to tailor modeling.

Scientific Applications:

• Structural characterization of homo-oligomers: Provides predicted oligomer structures for interpretation of quaternary assembly and interfaces.
• Functional and mechanistic studies: Enables analysis of molecular bases of protein function and regulation in processes such as metabolism, signal transduction, and immunity.
• Drug discovery targeting oligomeric states: Supports identification of oligomer-specific interfaces and conformations relevant to therapeutic targeting.

Methodology:

Combines template-based modeling and ab initio docking with model refinement, and has been validated on benchmark sets and in blind assessments such as the Critical Assessment of protein Structure Prediction (CASP).