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  1. Jalview
  2. JAL-4458

parse PDB / mmCIF header/medata to improve autodetection of models, licensing and cross-references

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.3.0, 2.11.4.0
    • Fix Version/s: 2.12
    • Labels:
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      Description

      Jalview should be able to autodetect AlphafoldDB structures imported directly since they include text like the following in the TITLE and REMARK lines:

      HEADER 01-JUN-22
      TITLE ALPHAFOLD MONOMER V2.0 PREDICTION FOR TRIOSEPHOSPHATE ISOMERASE
      ..
      Licensing can be obtained from the REMARK:
      REMARK 1 ACADEMIC AND COMMERCIAL PURPOSES, UNDER CC-BY 4.0 LICENCE.
      Finally, 'UNP' refers to the Uniprot accession:
      DBREF XXXX A 1 253 UNP A0Q8C4 TPIS_FRATN 1 253

      So importing a pdb file like this should yield a sequence annotated with temperature factor interpreted as PLDDT automatically, and a database cross-reference to uniprot with the stated accession.

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: