3D-SURFER

3D-SURFER compares and analyzes protein surface shapes using 3D Zernike descriptors to identify structurally similar proteins and surface features.

Key Features:

• 3D Zernike Descriptor-Based Surface Comparison: Uses rotationally invariant 3D Zernike descriptors to efficiently compare protein surface shapes.
• Protein Data Bank Search: Enables comparison of query protein surfaces against structures in the Protein Data Bank (PDB).
• Multiple Structural Comparison Levels: Supports structural comparisons at the level of protein chains, domains, and complexes.
• Surface Representation Options: Allows comparison of all-atom surfaces and backbone-atom surfaces for structural analysis.
• Batch Structural Searches: Performs batch searches for large-scale protein surface comparisons.
• Protein Pocket Detection: Integrates VisGrid and LIGSITE(csc) to identify potential binding pockets on protein surfaces.

Scientific Applications:

• Protein Function Annotation: Predicts functions of uncharacterized proteins by identifying structural surface similarities with known proteins.
• Drug Discovery: Detects surface pockets and binding sites for structure-based drug design.
• Protein Structural Analysis: Enables comparative analysis of tertiary structures based on protein surface geometry.

Methodology:

The method represents protein surfaces using 3D Zernike descriptors for rotationally invariant shape comparison, searches structural databases such as the Protein Data Bank (PDB), and identifies surface pockets using VisGrid and LIGSITE(csc).