Get fresh inspiration from this huge update of SeeSAR! We realized, on the one hand, that the functionality of the editor was growing and growing, making it more and more complicated to use. On the other hand, access to the full functionality of ReCore demands a different kind of user interface. So we "took the bull by the horns" and, akin to the editor, created the new Inspirator which you can use to do:
- core replacement
This feature is the same but with a much improved UI. You are able to directly select and visualize the bonds that will be clipped to carve out a core fragment for replacement. The clipped bonds now remain in place (even while you define sphere constraints) up until you define a new query. Also the display of results is much enhanced, as you can see the new core fragments highlighted in 2D as well as in 3D. For reference, your query molecule stays visible as well.
- fragment linking and merging
You may of course launch the Inspirator with more than just one molecule. In this case, you can define bonds to clip on different molecules, thereby requesting linker fragments that will connect the remaining pieces. Note that it is not mandatory to clip a terminal part of each molecule to create the query, you may replace a core part in one and connect it to another fragment at the same time.
- fragment growing
This was possibly the most frequently requested functionality in ReCore: Cut just one bond and grow onto this bond using a fragment library of typical side chains. In this way, you can, for example, reach out to nearby subpockets. The new growing algorithm can very quickly scan through a (for now) ready-made library of typical fragments. You may of course define sphere constraints at the same time in order to target particular locations in the binding site. Note that the new growing feature requires the download of a new ReCore index from here!
- other enhancements
- The biggest other enhancement is the new "Sequence View" window. You will have noticed that the binding site visualization dislog was always a bit crowded. As a first step towards a fully featured protein sequence view, the visualization of all binding site components (amino acids, ligands, water, metals) can now be controlled via the sequence view. But besides more space and a much cleaner interface, you may now see the binding site components of all loaded proteins.
- The editor has been enhanced in two ways. Firstly, it is now possible to flip side chains of central atoms. Naturally the demand for this feature came from the need to flip stereo centers, but we did not limit it to just these. Click on the central atom and cycle through the viable options, the flip then requires just one more click. Secondly, we have added the more rare elements Boron, Silicon and Selenium and ordered the list of elements in the menu according to in the periodic table.
- Normally users work on a particular computer with a particular setup (1 vs. 2 monitors, laptop vs. high-resolution big screen). So now you can arrange the layout of SeeSAR so that it best fits the geometry of your display hardware, such as the size of the different windows (whether all-in-one or docked out). SeeSAR stores these settings for you and next time it will open up any project using the same layout.