The Protein Geometry Database (PGD)

The Protein Geometry Database provides a database correlating protein backbone bond lengths, bond angles, and planarity with backbone conformation (φ, Ψ) to support analysis of protein structure and function.

Key Features:

• Comprehensive Querying Capabilities: Enables queries focused on conformation or backbone geometry independently as well as queries of their interrelationships.
• Assessment of Uniqueness: Enables evaluation of the uniqueness of specific conformational or geometric features observed within protein structures.
• Discovery of Novel Features and Principles: Provides systematic access to correlations between backbone geometry and conformation to facilitate identification of previously unrecognized structural patterns or principles.

Scientific Applications:

• Structural Biology: Analyze geometric constraints imposed by backbone conformations to study protein folding and stability.
• Protein Engineering: Identify unique geometric features to guide design or modification of protein scaffolds.
• Drug Design: Characterize conformational flexibility and geometric properties of target proteins to inform rational drug design.

Methodology:

PGD compiles a dataset correlating backbone bond lengths, bond angles, and planarity with backbone dihedral angles φ and Ψ.