ROCS - Shape Based Alignment for Virtual Screening

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Role-based/Computational Chemist

  • Product-based/ROCS

  • Solution-based/Small Molecule Lead-opt/3D Similarity

  • Solution-based/Virtual-screening/DB Search

  • Task-based/Virtual Screening - Ligand-Based

Description

ROCS aligns and scores a database of molecules to a shape query or a template molecule. The alignments can be used for a variety of purposes. The scores are used to rank molecules based on the probability that they share relevant (biological) properties with the query molecule.

ROCS aligns molecules based on their shape similarity and their distributions of chemical features. The minimal inputs into ROCS are a shape query or a query molecule with a single 3D conformation, and a search database of molecules with multiple 3D conformations.

Output from the ROCS floe is a hitlist with highly similar molecules at the top. Additional output data columns consist of individual shape and color similarity scores, as well as shape and color overlap diagrams for each alignment.

Promoted Parameters

Title in user interface (promoted name)

ROCS settings

ROCS/SubROCS/Random (start_type): To perform calculation with SubROCS or ROCS with inertial or random starts

  • Type: string

  • Default: Rocs

  • Choices: [‘Rocs’, ‘Subrocs’, ‘Random’]

Number of random starts (num_rand_starts): Number of desired starts in the random starts mode

  • Type: integer

  • Default: 4

Num Best Hits (best_hits): Number of best-scoring molecules to keep

  • Required

  • Type: integer

  • Default: 500

Sorter type (sorter_type): Type of predicate for sorting scores

  • Type: string

  • Default: HighestTanimotoCombo

  • Choices: [‘HighestTanimotoCombo’, ‘HighestFitTverskyCombo’, ‘HighestRefTverskyCombo’]

Generate Overlap Depictions (make_depictions): Whether or not to generate shape and color overlap depictions for each hitlist entry

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]

Color Force Field (color_ff): Color force field to be used

  • Type: string

  • Default: ImplicitMillsDean

  • Choices: [‘ImplicitMillsDean’, ‘ExplicitMillsDean’, ‘ImplicitMillsDeanNoRings’, ‘ExplicitMillsDeanNoRings’]

Custom Color FF File (custom_ff): Custom color force field file. Entry in this field overrides any other color force field selections

  • Type: file_in