ColBuilder

ColBuilder constructs full-atom models of cross-linked type I collagen fibrils to represent their native atomic structure for structural and functional analyses.

Key Features:

• Integration of multiscale data: Integrates low-resolution x-ray fiber diffraction with high-resolution x-ray crystallography and mass spectrometry data to build comprehensive full-atom models of collagen fibrils.
• Cross-link modeling: Incorporates multiple cross-link types and their localization within the fibril to represent native cross-linking patterns and support simulation of mechanical properties and interactions.
• Species diversity: Provides models for type I collagen from 20 different species to enable comparative analyses.
• Simulation facilitation: Supplies Amber force field parameters for modeled cross-links to enable molecular dynamics and structure-based simulations.

Scientific Applications:

• Structural analysis: Enable atomic-level exploration of type I collagen fibril structure, mechanical properties, and protein interaction networks.
• Disease modeling: Simulate different cross-link types and localizations to investigate how collagen structural alterations may contribute to disease.
• Comparative studies: Use models across 20 species to examine evolutionary differences and similarities in collagen structure and function.

Methodology:

Combines low-resolution x-ray fiber diffraction data with high-resolution x-ray crystallography and mass spectrometry data, builds full-atom models of cross-linked collagen fibrils, and provides Amber force field parameters for the modeled cross-links.