TBM

TBM integrates template-based modeling with free docking to predict protein–protein complex structures from sequences and structural templates using homology models and distance restraints.

Key Features:

• Template-Based Modeling (TBM): Leverages available structural templates to generate homology models and derive distance restraints for docking.
• Sequence input capability: Accepts sequences of component proteins as input rather than requiring pre-existing structures.
• Integration with free docking: Combines template-based restraints with free docking to reproduce interfaces suggested by weak or ambiguous templates while reducing incorrect predictions.
• Automated workflow: Automates template selection, homology model generation, restraint application, and docking steps.

Scientific Applications:

• CAPRI assessment (rounds 38–45): Applied to predict targets and interfaces evaluated in CAPRI rounds 38 to 45.
• Structural biology: Facilitates prediction and validation of protein–protein complex structures and interfaces.
• Drug discovery: Assists identification of interaction interfaces relevant for targeting protein–protein interactions.
• Bioinformatics research: Provides modeling approaches for studying protein–protein interactions using sequence and template data.

Methodology:

Use of available templates to generate homology models and distance restraints; acceptance of protein sequences as input; combination of template-derived constraints with free docking to produce and refine complex models.