Protein targets possess multiple potential association sites for binding ligands. One or more of these, depending on the protein target class, were meant by Nature to bind to polypeptide or small molecule endogenous ligands; agonists, antagonists, substrates, or cofactors for that protein. Others of these locii present new opportunities for modulating protein function, there being neither endogenous ligands for these sites nor known functional consequences for binding to these association sites.

TTPSite® computationally maps and annotates all possible and reasonable binding locii in protein target 3D models. These binding loci must be accessible by a small molecule from the protein surface and sized appropriately to efficiently bind small molecules. The ensemble of binding sites may include natural ligand/substrate or cofactor binding sites, or even known or unknown allosteric modulation sites. All can be employed in the next stage of TTPredict®, TTPDock®.