  The rapid growth in the number of experimental and predicted protein
structures and more complicated protein structures challenge users in
computational biology for utilizing the structural information and protein
surface property representation. Recently, AlphaFold2 released the
comprehensive proteome of various species, and protein surface property
representation plays a crucial role in protein-molecule interaction prediction
such as protein-protein interaction, protein-nucleic acid interaction, and
protein-compound interaction. Here, we proposed the first comprehensive
database, namely ProNet DB, which incorporates multiple protein surface
representations and RNA-binding landscape for more than 326,175 protein
structures covering 16 model organism proteomes from AlphaFold Protein
Structure Database (AlphaFold DB) and experimentally validated protein
structures deposited in Protein Data Bank (PDB). For each protein, we provided
the original protein structure, surface property representation including
hydrophobicity, charge distribution, hydrogen bond, interacting face, and
RNA-binding landscape such as RNA binding sites and RNA binding preference. To
interpret protein surface property representation and RNA binding landscape
intuitively, we also integrate Mol* and Online 3D Viewer to visualize the
representation on the protein surface. The pre-computed features are available
for the users instantaneously and boost computational biology development
including molecular mechanism exploration, geometry-based drug discovery and
novel therapeutics development. The server is now available on
https://proj.cse.cuhk.edu.hk/aihlab/pronet/.
