Compare Ligand Binding Sites Against Ready Database of Protein Sites (March 30, 2022)

Are you interested in comparing binding sites of your proteins to experimental structures from the Guide to Pharmacology, or to the popular models of human proteins predicted by AlphaFold2? This approach can help you identify possible side effects because of polypharmacology.

SiteHopper from OpenEye provides you with an innovative tool for comparison of ligand binding sites (patches) on proteins.

OpenEye offers three ready-to-use collections of SiteHopper patches. These highly curated collections cover experimental structures from the PDB and Guide to Pharmacology as well as AlphaFold2’s predicted structures of human proteins. The databases collectively contain ~40,000 known and ~300,000 potential binding sites:

  • Guide to Pharmacology Regular Patches: These are made up of patches of known protein—ligand binding sites.

  • Guide to Pharmacology Alternate Site Patches: This collection represents patches of potential binding sites predicted by our in-house tool OEPocket as well as F-pocket 4.0.

  • AlphaFold2v1 Human Alternate Site Patches contains patches of potential binding sites as predicted by OEPocket and F-pocket 4.0

Searching for proteins with binding sites similar to your targets in Orion is only a few mouse clicks away.

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This screenshot shows the query protein—ligand binding site of PDB # 4gih (green) and the highest scoring SiteHopper hit from OpenEye’s AlphaFold2v1 Human Alternate Site Patches collection (purple).

Tips:

See the documentation for more details on making a SiteHopper patch collection and on searching a SiteHopper database. A tutorial for running a SiteHopper search in Orion can be found here.