SiteHopper Search

Category Paths

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

• Product-based/SiteHopper

• Role-based/Computational Chemist

• Role-based/Structural Biologist

• Task-based/Target Prep & Analysis/Protein Similarity Search

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

Description

This floe performs a SiteHopper search on protein targets in a SiteHopper Collection. The search has two stages. (1) A pre-screen filters for target matches and (2) the rescore/refinement step generates a hit list of top performing searches.

SiteHopper compares protein binding sites between protein targets using shape and color. For more information see SiteHopper (to avoid leaving this page, right-click and open link in new tab)

Potential Input Sources SPRUCE - Protein Preparation, SPRUCE (to avoid leaving this page, right-click and open link in new tab)

Computation Scaling This floe has been optimized for search. The size or number of the SiteHopper Collection(s) will have little effect on computation costs.

Limitations This floe only accepts a single design unit as a query per run.

Promoted Parameters

Title in user interface (promoted name)

Inputs

Query dataset (data_in): Only a dataset with record as query is supported. If you supply a dataset with more than one record, or one record with more than one DU, the floe will fail.

• Required

• Type: data_source

Input Collections (collection): Collection containing SiteHopper DUs and Patch oez files. Search can only be run on a single input collection.

• Required

• Type: collection_source

SiteHopper Search Hit List (num_hits): Size of the hit list from SiteHopper search.

• Required

• Type: integer

• Default: 200

Outputs

Output Search Hits (ofs): Output records from the SiteHopper search hits. The query used in the search will be the first record in the dataset.

• Required

• Type: dataset_out

• Default: SiteHopper Search Results

Search Failures (fofs): Output records that failed SiteHopper search.

• Required

• Type: dataset_out

• Default: SiteHopper Search Failures

SiteHopper Options

Normalize & Rescore (norm_rescore): Normalize, re-score and re-transform patches

• Type: boolean

• Default: True

• Choices: [True, False]

Score Cutoff (cutoff): Minimum patch overlay score to pass a hit to the hitlist

• Type: decimal

• Default: 0.98

Max Sequence Similarity (max_seq_score): Proteins with a sequence similarity score > max_score get sent to the failure port.

• Type: decimal

• Default: 100.0