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SeeSAR: what's new?

2018-06-05

version 8.0

Significant changes and improvements in SeeSAR demand another major release and version 8 well deserves to be a major update. The biggest change is that we now provide full protein visualization support. While the focus of the tool is for the most part still on the defined binding site, you can now...: see the whole protein in all its glory! As always, a major update means that HYDE scores must be re-calculated to stay in line with the changes made in the underlying structures. We certainly believe that these enhancements are well worth it:

  • improved alignment
    So far aligning and superposing binding sites for multiple proteins has been restricted to very similar protein structures only. Quite a few users have provided their feedback where this has failed — thank you for that. We have re-worked the alignment engine and are able to handle all of the borderline cases we have seen. While the alignment is still suited to homologous proteins and similar binding sites only (we simply don't want you to compare apples with oranges), the limitations are far less severe, so we are quite confident that we have found a great compromise.
  • full protein support in the seqence view
    The sequence view has been enhanced a great deal. Most notably all components of proteins are visible and not just the components of the defined binding site (individual proteins, residues, small molecules, metals, waters, and chains). You can restrict the sequence view to show the defined binding site only (as before) but you now also have access to everything — plus a very convenient search feature.
  • bundled visualization controls
    So far the visibility of protein components could be toggled (show/hide) in two unrelated locations that were far apart in the UI: (a) the visualization settings top right and (b) the sequence view. For your convenience we have bundled all these visualization controls in the sequence view. In each of the tabs, protein components that can be shown or hidden are represented by items which all display the same behavior — namely: mouseover highlights the corresponding components in 3D and click toggles their visibility. A new reset view button allows you to go back to the visualization defaults.
  • enhanced pharmacophore handling
    Pharmacophores (namely sphere constraints) may be defined and used in different parts of SeeSAR. They can currently be used in the inspirator and for filtering in the molecules table, while in an upcoming version of SeeSAR they will be available for docking as well. The handling of sphere constraints has now been centralized so that the list of defined constraints is available globally in SeeSAR. Once a constraint has been defined, it is available to use everywhere. In addition, we have improved the consideration of sphere constraints during growing in the inspirator. Whereas the pharmacophore was previously applied as a post-filter to the final set of results, it is now actually used to guide the growing algorithm in generating suitable solutions that meet the constraint.
  • inspiration for covalent binders
    You may now also load covalent binders into the inspirator which means you can design — in a de novo fashion — covalent inhibitors using the core replacement, fragment merging and fragment growing technologies that are available in this mode. Particularly in conjunction with the enhanced application of pharmacophores (c.f. above), the growing option for covalent binders has become quite a powerful tool.

2018-03-29

version 7.3

2018-01-10

Inspirator version 7.2

2017-10-13

version 7.1

2017-09-12

version 7.0

2017-07-06

version 6.1

2017-06-19

version 6.0

2017-04-12

version 5.6

2017-01-12

version 5.5

2016-10-19

version 5.4

2016-08-26

version 5.3

2016-07-21

version 5.2

2016-06-27

version 5.1

2016-05-27

version 5.0

2016-03-17

version 4.2

2016-02-10

version 4.1

2015-11-18

version 4.0

2015-09-04

version 3.3

2015-07-24

version 3.2

2015-07-10

version 3.1

2015-04-14

version 3.0

2015-03-11

version 2.2

2015-01-26

version 2.1

2014-12-15

version 2.0

2014-11-03

version 1.6

2014-09-23

version 1.5

2014-08-21

version 1.4

2014-07-08

version 1.3

2014-06-16

version 1.2

2014-05-19

version 1.1