A lot has changed in this new version of SeeSAR, justifying again a major update release. Our focus this time lay on the editor — essentially this has now evolved to become a full-blown "Designer"! Read on below to find out all the details. Among other things, an update to the torsion distribution database as well as an improved intra-molecular clash test can lead to changes in the affinity estimations using HYDE, which is why any existing affinity estimations will be re-set if you read in a project file from an older SeeSAR version.
- Full integration of ReCore funtionality
Until now, the core replacement facility in the editor only scratched the surface of the powers of the ReCore algorithm. Now, the joining and merging of fragments is also possible. In order to do this, the editor can be launched with multiple molecules at once — the 2D view in the editor supports this feature too. In addition, you can fine-tune results delivered by ReCore using pharmacophore filters.
- Enhanced editing
Many users have asked for a ring building feature in the editor to make adding entire rings at once possible. We have now added this feature as part of the Add Atoms submenu. The menu contains a selection of the most common rings and once you have added one to your molecule, you can then choose the most appropriate ring conformation by examining the choices in the 3D view. This feature means that large changes can quickly and readily be made to molecules and this in itself necessitates another new feature in the editor — namely that (if you have defined a binding site) new poses can be generated for the edited molecule based on the conformation of the molecule before editing. The positioning is carried out using the overlay of the MCS between the pre-edited and edited molecules as a basis.
- Torsion distribution database update and display
On the one hand, we have now integrated the latest update of the database of torsion angle distributions from the CSD, while on the other, it is now possible to view the torsion angle distribution for a particular rotatable bond. This is shown in bond labels analog to the display of HYDE score information in atom labels. A click on the eye icon in this label highlights the atoms involved in the particular torsion pattern that identifies the torsion distribution information in the database.
- Miscellaneous enhancements
Several users have requested the possibility of saving their particular selection of favorites and any comments attached to a molecule via the SDF export. These are both now saved by default as SDF properties. Also, two filters can be added for numerical properties so that it is now possible to define both a lower and upper bound. Hydrogen bonds are now automatically hidden from view if the protein component of the hydrogen bond is hidden using the visualization settings in the toolbar. Last but not least, we have implemented a feature for measuring angles and torsions, besides distances.