Introducing Ultra-Fast Pocket Exploration with FastGrow in SeeSAR 12.1


Introducing Ultra-Fast Pocket Exploration with FastGrow in SeeSAR 12.1

June 24, 2022 11:15 CEST

We are proud to announce the introduction of FastGrow to SeeSAR 12.1 “Narcissus”. Being the world’s fastest app for this, FastGrow enables users to breathtakingly fast search for ligand decorations or extensions that complement unoccupied binding cavities of a target structure. Being developed at Hamburg University in a joint collaboration with Servier Paris and BioSolveIT, FastGrow has already partied first successes at AbbVie. Certainly, it has previously been thoroughly validated on real fragment growings/replacements in various scenarios. One example of these was to re-discover full complexes that had been automatically mined from the PDB and that correspond to chemical series found in literature. This novel tool shall enable interactively explorative growing and put control over the growing process firmly back into the user’s hand. Further, users can apply pharmacophore constraints to fine-tune their search according to their needs. The paper has just been submitted, and a command line version of the tool will be made available as well.

A library of 12,000 fragments is included by default in the 12.1 update and another, larger library with over 120,000 individual fragments is available as download for users who desire even more diversity and possibilities for their projects, completely free-of-charge. For those who want to use FastGrow with their own compounds and building blocks, a database creator is accessible that can create libraries compatible with the tool. Even for several hundred-thousands of fragments, a standard search with FastGrow in the Inspirator Mode requires only a few seconds runtime on standard hardware.

Additionally, a set of improvements found their way to the 12.1 update. Here are some excerpts:

Per default, SeeSAR will feature a ReCore index of 20,000 3D fragments for beginners. Other and much larger ReCore indices (CSD, PDB, ZINC, Magic Rings) are still available for download.

Furthermore, users will be able to control allowed conformations of six-membered rings within the Docking Mode and the Similarity Scanner.

If a ligand in a PDB file os annotated with “subject of investigation” / “ligand of interest (LOI)”, then SeeSAR will feature an additional indicator in the “LOI” column in the ligand extraction step for you.

Download SeeSAR 12.1 and start your pocket exploration today!