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 ~0.5 million 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.

You can screen any giga-sized library in ICM but we have the following conformers pre-prepared.

• Enamine REAL database
• NIH Synthetically Available Virtual Inventory (SAVI)
• WuXI Galaxi database

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.

icm _ride templates.ob|sdf input_3D_conf.molt output.sdf options Options:

• -e : penalize atoms outside the Envelope of the template(s)
• -o : weight templates atom by occupancy
• -shape: match shape only (all atoms are treated as the same type)
• APFcutoff= : skip compounds with normalized APF score above cutoff (VLS mode)
• exclude= : excluded volume points
• excludeMargin=(0.) : If envelope (-e) then atoms outside vw_radius + excludeMargin (outside envelope) will be penalized. If excluded volume (exclude=) is used atoms closer than ( vm_exvol_radius + vw_radius + excludeMargin) will be penalized (clash with envelope)
• Xweight=(3.) : repulsion weight of the 'eXcluded volume' atoms
• mnhits=(10000) : max number od hits with specified cutoff
• diCenter=(5.) : 'eccentricity' cutoff
• proc=() : number of threads
• effort=(1.) : effort>1 will use extra 'fine' map set for score and pose refinement
• fr= : scan entries starting from
• to= : scan entries to
• listjobs= : split the DB scan into and prints commands to launch them later

RIDE Results:

• Score: The Score is the sum of all atomic contributions to the overall Atomic Property Field (APF) score, plus any penalties (e.g., envelope or excluded volume). Each atom is assessed by how well its properties (such as hydrogen bonding, charge, hydrophobicity, aromaticity, and size) match the target environment. A lower score indicates a better fit.
• Strain: strain in kcal/mol - the lower the better
• NormScore: normalized by self Score. values: [0-1]