GalaxyHeteromer

GalaxyHeteromer predicts and refines protein heterodimer complex structures to provide atomistic models for the analysis of protein–protein interactions.

Key Features:

• Heterodimer structure prediction: Predicts heterodimer complex structures from input amino-acid sequences or provided subunit structures.
• Subunit modeling: When subunit structures are not available, employs template-based and distance-prediction modeling methods to generate monomer structures.
• Docking strategies: Performs template-based docking when suitable templates exist and ab initio docking when they do not.
• Template identification: Identifies templates in protein structure databases based on sequence and structural similarity.
• Template sources: Considers templates derived from monomer structures, homo-oligomers, and hetero-oligomers to leverage evolutionary relationships.
• Model generation and scoring: Generates multiple structural models for each predicted heterodimer and reports associated scores for evaluation and refinement.
• Atomic-level refinement: Refines predicted heterodimer structures to provide atomistic structural insights.

Scientific Applications:

• Protein–protein interaction analysis: Provides atomistic models to interpret and characterize protein–protein interactions.
• Functional hypothesis testing: Generates structural models to test mechanistic and functional hypotheses about protein complexes.
• Therapeutic and molecular design: Supports the design of therapeutic agents and novel functional molecules based on modeled interfaces.
• Disease mechanism investigation: Aids in understanding disease mechanisms by modeling disease-relevant heterodimer complexes.

Methodology:

Accepts input sequences or subunit structures; uses template-based and distance-prediction modeling to build subunits when needed; applies template-based docking or ab initio docking for heterodimer prediction; identifies templates by sequence and structural similarity in protein structure databases including monomers, homo-oligomers, and hetero-oligomers; generates multiple models and reports associated scores and performs atomic-level refinement.