User-centric design of a 3D search interface for protein-ligand complexes

Area of Science:

• Biochemistry
• Structural Biology
• Bioinformatics

Background:

• The Protein Data Bank (PDB) is a critical resource for structural biology.
• Identifying and characterizing protein binding sites is essential for drug discovery and understanding protein function.
• Existing search methods for binding sites can be challenging due to complex 3D input requirements.

Purpose of the Study:

• To present the updated frontend of the GeoMine search engine.
• To introduce new features that simplify the geometric querying of protein binding sites.
• To enhance user experience for searching both known and predicted binding sites.

Main Methods:

• Development of a new 2D query editor synchronized with the existing 3D editor.
• Implementation of template-free query generation and template-based query selection in 2D.
• Integration of predicted empty binding sites from AlphaFold structures as query templates in the 3D editor.

Main Results:

• GeoMine's latest version simplifies geometric binding site searches through intuitive 2D input.
• The 2D editor offers full synchronization with the 3D editor, providing consistent functionality.
• Support for predicted binding sites in AlphaFold structures expands the search capabilities.

Conclusions:

• The enhanced GeoMine frontend significantly improves the accessibility of geometric binding site searches.
• The new 2D query formulation addresses user challenges with complex 3D input.
• GeoMine, available on ProteinsPlus, offers a powerful and user-friendly tool for exploring protein binding sites.