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Archive for the ‘target’ tag

Retrieving Target Classifications from ChEMBL

without comments

There are a number of scenarios when it’s useful to be able to classify protein targets – high level summaries, enrichment calculations and so on. There are a variety of protein classification schemes out there such as PANTHER, SCOP and InterPro. These schemes are based on domains and other structural features. ChEMBL provides it’s own hierarchical classification. Since I use this from time to time, it’s useful to pull all the classifications for a given species, at one go via the SQL below (tested with v17):

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SELECT
    td.pref_name, description, accession, pfc . *
FROM
    target_dictionary td,
    target_components tc,
    component_sequences cs,
    component_class cc,
    protein_family_classification pfc
WHERE
    td.tax_id = 9606 AND td.tid = tc.tid
        AND tc.component_id = cs.component_id
        AND cc.component_id = cs.component_id
        AND pfc.protein_class_id = cc.protein_class_id;

Written by Rajarshi Guha

July 23rd, 2014 at 1:30 pm

Posted in cheminformatics,software

Tagged with , , ,