Database Commons

a catalog of worldwide biological databases

The openly accessible ProteinsPlus web server at https://proteins.plus is a unique resource enabling protein structure mining and modeling, focussing on protein-ligand interactions. Since its launch in 2017, the number of tools is steadily increasing. Currently, the server comprises six methods for protein structure analysis, four tools for mining the Protein Data Bank (PDB), and five prediction approaches regarding protein-ligand complex modeling. Users can use experimental structures from the PDB or computationally predicted structures from the AlphaFold Protein Structure Database as starting points. Alternatively, they can upload individual structure files. Recent updates include novel methods for detecting binding sites and predicting solvent channels in crystallographic structures, as well as updates of tools for protein-ligand interaction depiction in 2D and binding site mining. Given these updates, we present a real-life application scenario that underpins the novelties and applicability of the web server's tools for modern structure-based design projects. It also highlights the next steps for the web server, which will be redesigned using a different technology stack to improve the inter-usability of the tools, ease maintainability, and make it future-proof.