Fingerprint Search - Small Scale 2D Similarity

Category Paths

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

  • Role-based/Medicinal Chemist

  • Solution-based/Virtual-screening/DB Search/2D Similarity and SubSearch

  • Task-based/Library Prep & Design/Substructure & Similarity Search

  • Role-based/Computational Chemist

  • Product-based/GraphSim

Description

Fingerprint Search - Small Scale 2D Similarity is a tool for finding similarity between an input dataset of molecules to a query or template molecule, based on molecular fingerprints.

The minimal inputs into 2D Similarity are a query molecule and a search database of molecules both in either 1D (SMILES), 2D (SD, mol2) or 3D format.

The output from the 2D Similarity floe is a hitlist with highly similar molecules at the top.

Promoted Parameters

Title in user interface (promoted name)

Similarity Field Names

Input Molecules Field (Input Molecule Field): The name of the field on the input records that stores the molecules compared to the query molecule. If left blank, the primary molecule field will be used.

  • Type: field_parameter::mol

Query Field (Query Molecule Field): The name of the field on the initialization record that stores the query molecule. If left blank, the primary molecule field will be used.

  • Type: field_parameter::mol

Query Molecule Title Field (query_molecule_title_field): The title of the query molecule used to obtain the score.

  • Required

  • Type: field_parameter::string

  • Default: Query Molecule Title Field

Similarity Score Field (Similarity Score Field): Name for the field that stores fingerprint similarity scores.

  • Required

  • Type: field_parameter

  • Default: Similarity Score

Similarity Parameters

Minimum Similarity Score (similarity_score_cutoff):

  • Type: decimal

  • Default: 0.0

Size cutoff (Size Cutoff): Used for performance optimization. Below this size, query molecules are passed to the similarity cube initialization port.

  • Required

  • Type: integer

  • Default: 10000

Fingerprint Type (fingerprint_type): The fingerprint type generated for similarity calculation.

  • Type: string

  • Default: Tree

  • Choices: [‘Circular’, ‘Lingo’, ‘MACCS’, ‘Path’, ‘Tree’]

Deduplicate Results (Deduplicate Dataset): If set to True, if multiple input molecules are the same, retain only similarity result for the query molecule with the highest score.

  • Required

  • Type: boolean

  • Default: True

  • Choices: [True, False]

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

  • Required

  • Type: integer

  • Default: 500