Macs in Chemistry

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SeeSAR Updated to 2.0

 

SeeSAR has been updated to version 2.0. SeeSAR is a really interesting tool for ligand design, it enables users to explore lingered interactions in a real-time manner. There is a review of SeeSAR here. BioSolveIT have taken a strategic decision to provide rapid and regular incremental updates which means it is always worth checking to get the latest version. However this looks to be a rather more significant update.

seesarjan2015

This update of SeeSAR qualifies as a major release, since it covers a milestone in its development. So far SeeSAR was able to assess given poses of small molecules in a protein structure. Starting with release 2.0 SeeSAR can also generate poses. Also note that the Hyde affinity assessment behind the scenes has been further improved by a variety of fixes and small changes for the benefit of more stability of the calculations. These changes may have an effect on the computed scores. If you rely on the scores resulting from a scecific version of the tool, we recommend to keep such older versions of the tool in an archive.

Pose generation SeeSAR assesses the binding affinity based on the given position of the ligand in the active site. New in major release number 2 is the introduction of ligand pose generation directly within SeeSAR. So now you can draw and save a molecule in 2D, load it and have SeeSAR predict both binding poses and the related affinity for those poses. Similarly, if you make a substantial modification to the ligand in the editor, you can now validate the original position by generating new binding poses followed by the affinity assessment.

Ring conformation sampling Significant conformational changes occasionally occurred when ring atoms were modified, reducing confidence in the Hyde estimated binding affinity. We have overcome this by implementing a conformational sampling of ring systems to identify the closest of all energetically favorable ring-conformations.

Stay focused Sometimes, the “big picture” can get lost while browsing and inspecting poses in 3D – users can now reset to a standard orientation by hitting "Space" on the keyboard or with a click on the center view button in the toolbox (located in the lower right corner).

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