SEA Search Guide

Run SEA search in 3 easy steps:

• Step 1: Select fingerprint for the search

• Step 2: Select reference targets

  Select "Targets from ChEMBL library" to run search with all reference ChEML targets or restrict to a number of ChEMBL target by click on "Restrict to a subset of library targets"OR Select "Custom Targets" to run search with a user-specified list of target-compound activities that define one or more targets. Example:
  

                  Custom Target Format: (target_id) (smiles) (compound_id)
  
                  e.g.:
                  HCA1 C[C@H](O)C(=O)O lactate
                  HCA1 O=C(O)CCCO GHB
                  HCA1 O=C(O)c1cccnc1 niacin
                  HDAC1 C[C@@H](O)CC(=O)O BHB
                  HDAC1 [O-]C(=O)CCC butyrate
              

• Step 3: Select Query

  Select "ChEMBL Targets Query" to restrict search to a specific target subset OR Select "Custom Query" to defined list custom compounds or custom targets. Example:
  

                  Custom Compoumd Format: (smiles) (compound_id) or just ZINC ID
  
                  e.g.:
                  ZINC000431131405
                  ZINC000276896078
  
                  NCCc1c[nH]c2ccc(O)cc12 serotonin
                  NCCc1ccc(O)c(O)c1 dopamine
                  Oc1ccc(cc1O)[C@@H](O)CNC
                  NC[C@H](O)c1ccc(O)c(O)c1
              

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SEA Use Cases

Compounds vs. Targets

Purpose: User has one or more compounds of interest, such as one that has come out of a phenotypic screen and wants to predict its mechanism of action.

Case 1 + 2: Query Custom Compounds vs Reference Library Screen or specified library target(s)

Return a table where of predicted targets and te most similar annotated to the query target when a compound in a predicted target is select.
By clicking on the link under compound will take user to the /compound_vs_target which display the result in the heatmap

Case 3: Query compounds vs reference Custom Target(s)

Same as Case 1, the user specifies a list of target-compound activities that define one or more targets

Target(s) vs Targets

Purpose: The user want to compare the ligand similarity between two targets

Case 1 + 2: Query Custom Target(s) vs Reference Library Screen or specified library target(s)

Return a result table summarizing for each target in the library or subset of the library to the custom target(s)

Case 3: Query Library Target(s) vs Reference Library Screen

Same as above, but instead the search uses subset of library as query

Case 4: Custom target(s) vs [target, library screen, specific library targets]

Same as above except the user can define the targets by specifying the target name and the active compounds (one pair per line)