Kotai Antibody Builder

Kotai Antibody Builder constructs three-dimensional models of antibody variable regions to support structural analysis and antibody engineering using sequence alignment, canonical rules, and evolutionary information.

Key Features:

• Hybrid Template Selection: Integrates sequence alignment and canonical rules to identify suitable structural templates for antibody variable domain modeling.
• 3D Rendering of Alignments: Translates aligned antibody sequences into preliminary three-dimensional models of the variable region.
• CDR-H3 Loop Modeling: Predicts CDR-H3 conformations using rule-based heuristics including H3-rules derived from evolutionary data, with an optional refinement using fragment assembly and knowledge-based scoring.

Scientific Applications:

• Antibody Design and Engineering: Provides 3D variable-region models to inform sequence modifications and design choices for therapeutic antibody development.
• Structural Biology Studies: Supports analysis of the structural basis of antigen recognition and binding by antibody variable domains.
• Benchmarking and Validation: Enables model validation and benchmarking, with demonstrated performance on targets from the Second Antibody Modeling Assessment comparable to semi-automated expert-guided predictors.

Methodology:

Uses sequence alignment and canonical rules for hybrid template selection, performs 3D rendering of alignments, constructs initial CDR-H3 models with rule-based heuristics (including evolutionary H3-rules), and refines models via fragment assembly followed by knowledge-based scoring.