SeeSAR has been updated, the description below gives full details.
This update of SeeSAR qualifies as major release 4, as several milestones have been achieved with it - namely the integration of the world-renowned ADME property calculator from Optibrium™, the display of the protein surface in the 3D view, and an update of the Hyde scoring function. Collectively, these changes have made an update of the SeeSAR storage mechanism necessary, so unfortunately old project files cannot be loaded with this version. We recommend you save your molecules from old projects to file and re-read them with this new SeeSAR version. As an additional bonus feature we implemented the multi-selection of favorites with a simple [Shift] and click. Just try it out, it works as you would expect.
As of version 4.0, SeeSAR is equipped with an interface that allows you to benefit from Optibrium's ADME property calculator from within SeeSAR. Any molecule loaded or edited is passed on to the property calculator, which itself applies multiple computational models to determine a variety of ADME properties. By default you'll see:
logD @ pH7.4
logS (thermodynamic, intrinsic aqueous solubility)
logS @ pH7.4 (in phosphate buffered solution)
Blood-brain barrier penetration (log([blood]:[brain])
hERG inhibition (pIC50)
CYP2C9 affinity (pKi)
Human intestinal absorption (HIA) classification
Blood-brain barrier penetration classification
CYP2D6 affinity (pKi) classification
Plasma-protein binding classification
P-gp transport classification
However, if you have additional models (within the Optibrium framework) you can add those too and have the respective values available at your fingertips. Note that the usage of this feature requires a separate license!
The binding site of a protein is oftentimes quite complex making it easy to lose the sense of depth, space and tightness of fit. The protein surface of the binding site is now available to aid with orientation and can be toggled on and off very simply using a switch underneath the molecules table. This way, it is easy to switch between the surface view to find the orientation when you need to and the atom-only view at other times.
Hyde is quite sensitive with regards to the numerical stability of the calculation, which we have significantly improved with this update. We also detected a small inaccuracy in the way the coverage of interactions is calculated which has now been corrected. Overall Hyde now has a higher hit rate with respect to the experimental data for high-quality structures and on average avoids overestimating the affinities, i.e. it now provides a more conservative estimate thereby reducing the rate of false positives.