Substructure Search - Small Scale Substructure Matching

Category Paths

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

  • Role-based/Medicinal Chemist

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

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


Substructure Search - Small Scale Substructure Matching finds molecules containing patterns of interest, defined by MDL queries, from a database of molecules.

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

The output from the Substructure Search floe is a hitlist with the least complex molecules at the top.

Promoted Parameters

Title in user interface (promoted name)

Substructure Search Settings

Num Best Hits (best_hits): Number of least complex molecules to keep

  • Required

  • Type: integer

  • Default: 500

Selection Tag (query_tag): Tag to put on atoms to indicate selection

  • Type: string

  • Default: query

Match Tag (match_tag): The tag that is used to identify matched atoms and bonds.

  • Required

  • Type: string

  • Default: selected