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SeeSAR: one minute tutorials

60 seconds to ...

... improve your ligand!

In SeeSAR it takes only seconds to gauge how a modification on your ligand affects the binding affinity (or other physics-chemical properties). Simply edit the molecule in the pocket of a protein and save it to the table. Labels will help you to understand more deeply what the change is composed of. Within a minute you can easily find an improved compound.

... find a new scaffold!

In SeeSAR it takes only seconds to do a scaffold replacement. Within a minute you can easily find a scaffold-hop with optimized binding affinity. Simply go into the Inspirator, carve out the unwanted core, press a button and instantaneously see results populating the table. Sorting by affinity will flush the best scoring ideas to the top.

... explore your protein!

In SeeSAR it only takes 60 seconds to get a good feel for your protein. Whether you work in the active site of your existing ligand, or you want to explore an alternative (also allosteric) site, SeeSAR lets you do that in just a minute.

... link two fragment binders!

In just under a minute you can join two fragments in SeeSAR. Simply add the fragments to the Inspirator and select a bond vector on either one. SeeSAR will then find the missing link between them, without distorting the overall geometry too much. By saving the fragments to the table, the best scoring ones can be brought to the top and explored.
(Note that the HYDE affinity estimation has been accelerated for this presentation.)

... discriminate between multiple poses of one compound!

When analyzing docking data it can be a challenge to identify the likely "correct" pose for a molecule, particularly if the predicted affinities are very close together. Visualizing the tightness-of-fit shows you if there are gaps in the binding interface. The tighter the fit, the more likely it is you have the correct pose. Within less than a minute you identify false positives and may zoom in on your best bet.

... improve your ligand's hERG inhibition!

In SeeSAR you can monitoring hERG or other ADMET properties easily. As you interactively modify your ligand you will see live how a change affects the affinity and other properties of interest in the ligand table. Learn how this helps you do a complex multi-parameter optimization within just one minute.

... find out how well experimental and calculated affinities agree!

Particularly at the start of a new project and if some experimental data is already available, you may want to know how well the HYDE-estimated affinity agrees with the experimental data (mind the error-bars!). This may lead to the best choice of alternative protein structures or the detection of systematic errors. Simply load the experimental values together with your ligands into SeeSAR and then invoke the "performance check" to see which fraction matches, and which one is under- or overestimated.

... grow from fragment binder to explore your pocket!

If you have a fragment binder and know your synthesis options around it, load it into the Inspirator and select a bond vector off of your fragment. Growing speedily scans SeeSARs internal fragment library by flexibly attaching them. Calculated affinities (and other properties) help you identify the best proposed new compounds for follow up.
(Note that the fragment growing calculation has been accelerated for this presentation.)

... assess the conformation of a molecule!

SeeSAR helps you quickly analyze the conformation by color coding the rotatable bonds according to how well they are represented in the Cambridge Structural Database (CSD). This will not only alert you about outlier conformations, but also how much you can trust a generated pose, and further to discriminate good from bad poses.

... do a virtual hit-triage!

SeeSAR helps you triage your hits with a number of powerful filter functions that can be combined in an endless number of ways. Filter by affinity, hERG value, conformational stability, LLE or LE and many other physics-chemical properties until you have a manageable number of compounds for visual inspection, selection and synthesis.