GalaxyWEB

GalaxyWEB predicts three-dimensional protein structures from amino acid sequences using template-based modeling combined with ab initio refinement to support structural interpretation of protein function.

Key Features:

• Template-based modeling: Predicts protein structures by aligning target sequences to existing templates from known protein databases.
• Multiple-template integration: Integrates multiple template sources to construct reliable core structures in regions with homologous sequences.
• Ab initio modeling for loops and termini: Applies ab initio modeling to refine variable loop and terminus regions that lack reliable templates.
• Optimization-based refinement: Employs an optimization-based refinement method to improve accuracy of predicted structures, especially in challenging regions like loops and termini.
• Refinement-only mode: Accepts pre-existing models with specified loop or terminus locations for targeted refinement.
• CASP9 validation (Seok-server): The methodology was recognized as a top-performing server in CASP9 under the name "Seok-server".

Scientific Applications:

• Drug design: Provides structural models to support rational drug design and ligand-binding analysis.
• Functional annotation of proteins: Enables inference of protein function and regulatory mechanisms from three-dimensional structures.
• Protein–protein interaction analysis: Supports analysis of interaction interfaces in protein–protein interactions.

Methodology:

Uses template-based modeling with templates from known protein databases, integrates multiple templates to build core regions, applies ab initio modeling for loops and termini, and performs optimization-based refinement.