ProNet DB

ProNet DB provides a proteome-wide database of protein surface property representations and RNA-binding profiles to support prediction and analysis of protein–molecule and protein–RNA interactions.

Key Features:

• Extensive Protein Structure Collection: Contains 326,175 protein structures including proteomes of 16 model organisms from the AlphaFold Protein Structure Database and experimental structures from the Protein Data Bank (PDB).
• Detailed Surface Property Representations: Provides per-protein surface property representations including hydrophobicity, charge distribution, and hydrogen-bonding potential.
• RNA-Binding Landscape Integration: Includes RNA-binding site annotations and binding preference profiles to characterize protein–RNA interactions.
• Interacting Faces Identification: Annotates interacting faces on protein surfaces to support analysis of molecular interfaces.
• Visualization Tools: Supports visualization of protein structures and surface representations via Mol* and an Online 3D Viewer.
• Pre-computed Features: Provides pre-computed surface properties and RNA-binding annotations across the dataset.

Scientific Applications:

• Molecular Mechanism Elucidation: Facilitates analysis of protein interaction mechanisms through surface property and interface annotations.
• Geometry-Based Drug Discovery: Enables geometry-based drug discovery by supplying structural surface descriptors relevant to ligand binding.
• Novel Therapeutic Approaches: Supports exploration of therapeutic strategies that target protein–RNA interactions by integrating RNA-binding profiles.

Methodology:

Processes structural information from AlphaFold2 and the Protein Data Bank (PDB) and integrates multiple protein surface representations with RNA-binding landscapes.