Target Exploration Overview Tutorial

The Target Exploration Module consists primarily of the Cryptic Pocket Detection floes and additional support floes. Target exploration involves the identification of novel targets that may be difficult to detect.

The general progression of investigation in this module is as follows.

1. Prepare a protein using the SPRUCE — Protein Preparation floe or use data from MMDS. MMDS is an OpenEye protein structure repository of proteins from experimental data for structure-based discovery.

   1. A fully prepared protein is essential for the next steps of this tutorial. Protein preparation using Spruce will process PDB or mmCIF files containing the structures into molecules usable for molecular modeling.

2. Run a Cryptic Pocket Detection floe. The cryptic pocket floes seek to uncover hidden binding sites of proteins, to assess the druggability of difficult targets.

3. Run a SiteHopper floe. SiteHopper compares protein binding sites. It first converts a binding site to a searchable site called a patch, which it compares to other binding site patches, which are stored in a pregenerated database. Make SiteHopper Patch Database generates a SiteHopper patch collection. SiteHopper Search generates a hit list of top performing searches.

Note

More detailed module-level tutorials will be provided in a later release.