Small Molecule Modeling

v2.1.1 August 2025

This package is built using OpenEye-orionplatform==6.5.1, OpenEye-toolkits==2025.1.0, and OpenEye-Snowball==0.30.0.

The OEDocking - Dock into an Active Site for Virtual Screening Floe has the following updates:
- There is an option to fail optimized poses for excessive bending of aromatic rings in the Refined and STMD quality options.
- The AUTO docking mode now uses FRED or HYBRID for docking based on the similarity of the molecule to the bound ligand.
  - FRED is used if the receptor is apo, or if the molecule has low similarity to the bound ligand.
  - HYBRID is used if the receptor is holo, and if the molecule has high similarity to the bound ligand.
- You can now use the same protein mask in the Docking, Optimization, and Check Clashes Cubes.
- These changes have been made in the STMD mode. You can now:
  - Generate 50 poses using exhaustive docking with FRED.
  - Perform pose clustering before optimization (in addition to one after optimization) using the ChemGauss4 Score for ranking the pose before optimization, and an RMS threshold of 1.0 for deduplication.
  - Perform deduplication of a pose as it is, without doing any overlay.
The SZYBKI - Ligand Minimization in a Rigid Active Site Floe and SZYBKI - Ligand Minimization in a Flexible Active Site Floe have a new parameter, bent_ring_check, to set whether or not to fail the optimization when there is excessive deviation from planarity in aromatic rings.