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RIDE - Rapid Isostere Discovery Engine



RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields, developed at MolSoft. RIDE searches databases of compound conformers for molecules that are isosteric to the query, i.e. have similar 3D configurations and distributions of atomic properties.RIDE is available in the ICM-Pro + VLS package.

The GPU-based implementation is capable of searching ~0.5mln conformers/second on a single GPU card and perform 3D virtual screens of millions of compounds with the level of interactivity comparable to 2D searches. VLS benchmarking on DUDe indicates that RIDE searches produce enrichments on par with much slower standard flexible APF VLS.

RIDE applications include:

  • Virtual screening - efficiently screen "giga-sized" libraries.
  • Scaffold hopping - discover structurally novel chemicals based on a lead.
  • Hit follow-up - quickly discover new chemicals with similar 3D pharmacophoric binding properties to your lead.
  • Core replacement in the ICM 3D ligand editor.

A simple web-based interface is provided for the ease of use by chemists, while batch script may be used by chemoinformatitians. In either format, RIDE allows fine-tuning of the queries to generate most desirable hit lists. This includes:

  • Atom Weighting - Contributions of different portions of the molecule can be modulated with per-atom weights to reflect relative importance of certain moieties.
  • Excluded Volumes meet Shape Matching - An envelope penalty can be applied to the regions that surround all or part of the query molecule to prioritize hits without bulky extensions in constrained regions.

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