RosettaAntibody

RosettaAntibody predicts three-dimensional structures of antibody variable regions from light and heavy chain amino acid sequences using template-based modeling and high-resolution refinement.

Key Features:

• Template-Based Homology Modeling: Identifies homologous templates for framework regions and complementarity-determining region (CDR) loops, assembles side-chain–optimized crude models, and refines structures including CDR H3 loop modeling.
• High-Resolution Structural Sampling: Generates 2,000 independent variable region models, optimizes CDR backbone torsion angles and light–heavy chain orientation, and ranks the top 10 models using a Rosetta scoring function.

Scientific Applications:

• Antibody Structure Prediction and Docking: Supports antibody–antigen docking studies and rational antibody design through high-resolution structural models of variable regions.

Methodology:

RosettaAntibody performs sequence homology searches to select structural templates, assembles framework and CDR loop models, applies high-resolution refinement including CDR H3 modeling and steric clash minimization, generates large ensembles of structures, and ranks models using energy-based scoring.