OEDOCKING 4.2.0¶

Fall 2022

New features¶

The Posit application now uses the new OEShapeFit API for flexible fitting with Shape/Color and Forcefield. The new algorithm replaces the currently existing ShapeFit algorithm that uses adiabatic optimization. A modified ShapeFit algorithm optimizes the shape and chemical similarity between the fit molecule and bound ligand present in the reference design unit, along with intra-molecular forcefield energies of the fit molecule. The SAGE ligand force field is used during this optimization.
Spruce Filter was added to MakeReceptor, to assist in structure standardization prior to structure preparation.

Two new preliminary API classes, OEShapeFit and OEShapeFitResults have been added which provides functionality for pose generation based on flexible fitting with Shape/Color and Forcefield.
The adiabatic optimization algorithm of ShapeFit method for pose generation in OEPosit has been replaced by a new simultaneous flexible fitting algorithm, as implemented in OEShapeFit. The new algorithm uses Sage as the default forcefield, instead of MMFF.
Two new methods, SetFlexiOverlayOptions and GetFlexiOverlayOptions, have been added to OEPositOptions to expose parameters related to OEShapeFit in OEPosit.

An issue that caused a segmentation fault when using CacheScoringSetup has been fixed.

New C++ and Python examples have been added to the Flexible Overlay Optimization with OEShapeFit API section that demonstrate how to flexibly fit input multi-conformer molecules into a design unit that contains a bound ligand.