ProBiS-Fold annotates AlphaFold human protein database with

  • Binding sites for: compounds (small molecules), cofactors, proteins, peptides, nucleic acids, metal ion and conserved water
  • Post-translational modification sites (glycosylation sites)
  • Predicted ligands and glycosides for each binding site (3D structures as bound to protein)

ProBiS-Fold aims to

  • Provide interactive, downloadable binding sites for human proteome for functional and drug discovery studies
  • Enable human proteome-wide structure-based virtual screening and selectivity prediction

Binding sites and post-translational sites types

  • Compound (substrate/agonist-competitive ligands), cofactor (cofactor and cofactor-competitive ligands) (based on list of known cofactors), protein (both <20 aa. and >=20 aa.), peptide (<20 aa.), nucleic acid (DNA or RNA molecules), metal ion (structurally conserved) and water (structurally conserved)
  • Glycoslyation sites (O- and N- glycosylation)
  • Ranked according to the estimated druggability score (applies to compound and cofactor sites)


  • Centroids (x,y,z,radius) that accurately describe the often convoluted binding site shapes
  • Binding site protein residues that interact with ligands
  • Predicted ligands obtained using structure-based comparative ProBiS approach from similar binding sites in the PDB
  • Binding site bounding box (in AutoDock Vina format) ready for docking
  • Receptor, an AlphaFold2 predicted protein single chain structure


  • AlphaFold ID, UniProt ID, PDB ID and Chain ID (where available)
  • Protein name
  • Protein function, such as, protein kinases or cancer-related proteins
  • Binding site type and binding site rank
  • See tutorial for more query options

Download binding sites as

  • Individual or multiple selected binding sites based on user query (see tutorial for how to efficiently use the search bar on top of the page)
  • Prepared binding site datasets