Fetch ligands

This protocol extracts the ligands related to a SetOfDatabaseIDs. It defines 3 levels of relation depending on the database IDs:

  • UniProt IDs: using their cross references with an specified database, it will relate each UniProt ID to a number of target structures and extract their ligands.

  • Target IDs: the IDs refer to a protein target. The protocol will extract all ligands found in the structure.

  • Ligand IDs: the IDs refer directly to the IDs of the ligands in the specified database.

Note

In a second section, you can define several filters for the extracted ligands, from general ones according to the ligand structure to more specific depending on the chose database.

Input

Note

All parameters include a help button that gives further information for each of them.

Fetch ligands form 1

Fetch ligands form 2

The result of this protocol is a SetOfSmallMolecules with the extracted ligands.

Test

This protocol has an integrated test that can be run using the following command:

scipion3 tests pwchem.tests.tests_databases.TestFetchLigands