Time to Fall in Love with SeeSAR 12 – Narcissus

Explore the Beauty of Molecular Shape

After decades of structure elucidation, knowledge about the exact binding mode of a ligand remains a scientific luxury of the few. As a result, projects sometimes have to start from a single lead molecule without the possibility to rely on structural information about its interactions with the target. But how to proceed without knowing where to go? How to connect molecular features between unrelated scaffolds?
The answer: Embrace the beauty of what is already there.

SeeSAR 12, code-name 'Narcissus', enters the field of ligand-based drug discovery (LBDD) where the target's structure becomes an optional supplement.

A New Playground:
Introducing the Similarity Scanner

SeeSAR 12 features the new 3D mode 'Similarity Scanner'. It allows users to enter the world of LBDD by calculating and comparing 3D similarities of a template molecule with a ligand screening set — without the need of any structural information.
Powered by information about volume, shape, and pharmacophore properties of molecular structural elements, the Similarity Scanner generates superpositions of molecules on a selected template. A specialty of the algorithm is that we also align where interactions in 3D coincide. Users can interpret the visual output and use the provided similarity score to rank the results and cherry pick for compounds sharing interesting overlaps with the ligand of interest. This versatile method can be used as a new way of screening for potential actives and for scaffold hopping approaches.

More than Simple Conformer Alignment

The Similarity Scanner does more than only aligning two molecules based on substructures or volume: It further matches molecular features of the query molecule with its counterpart. This includes hydrogen bond acceptors and donors, aromatic and charged groups, and much more. Such coinciding interaction areas play a crucial role for a ligand-based screening approach, as the output will be enriched with results that can match the pharmacophore 'architecture' of the known active input molecule.

Augment Your Search Results

What you consider important may be made important for the Similarity Scanner. By applying pharmacophore constraints you can guide the screening and filter for poses that possess important molecular features.
The Similarity Scanner can furthermore be used as an additional scoring method for enrichment boosts after docking, or after searches across vast Chemical Spaces (e.g. following an infiniSee search).

Molecule Table Enhancement

The most beautiful SeeSAR of all time comes with a major redesign of compound handling in the tables. The frontline of the table now features all interactive elements in one place. Important molecules can be easily compared and colored, bulk processing can be achieved in one click with additional icons in the menu, and active and inactive molecules can be distinguished at first glance. Furthermore all those parameters including annotations and favorites can be sorted directly in the table.

SeeSAR 12 — the Beauty of Shape with 'Narcissus'

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