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  1. Jalview
  2. JAL-4311

properly handle sources other than alphafold providing PLDDT confidence scores & shading from model quality score type response

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    Details

    • Type: Improvement
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.3.0
    • Fix Version/s: 2.11.4
    • Component/s: Structures
    • Labels:
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      Description

      Any structure with 'pLDDT' model quality score should get alphafold2-style shaded alphafold reliability annotation tracks via JAL-3895, and be ranked along side other alphafold2 scored sources.

      See for example
      >EPAS1_HUMAN/1-870 Endothelial PAS domain-containing protein 1
      MTADKEKKRSSSERRKEKSRDAARCRRSKETEVFYELAHELPLPHSVSSHLDKASIMRLAISFLRTHKLLSS
      VCSENESEAEADQQMDNLYLKALEGFIAVVTQDGDMIFLSENISKFMGLTQVELTGHSIFDFTHPCDHEEIR
      ENLSLKNGSGFGKKSKDMSTERDFFMRMKCTVTNRGRTVNLKSATWKVLHCTGQVKVYNNCPPHNSLCGYKE
      PLLSCLIIMCEPIQHPSHMDIPLDSKTFLSRHSMDMKFTYCDDRITELIGYHPEELLGRSAYEFYHALDSEN
      MTKSHQNLCTKGQVVSGQYRMLAKHGGYVWLETQGTVIYNPRNLQPQCIMCVNYVLSEIEKNDVVFSMDQTE
      SLFKPHLMAMNSIFDSSGKGAVSEKSNFLFTKLKEEPEELAQLAPTPGDAIISLDFGNQNFEESSAYGKAIL
      PPSQPWATELRSHSTQSEAGSLPAFTVPQAAAPGSTTPSATSSSSSCSTPNSPEDYYTSLDNDLKIEVIEKL
      FAMDTEAKDQCSTQTDFNELDLETLAPYIPMDGEDFQLSPICPEERLLAENPQSTPQHCFSAMTNIFQPLAP
      VAPHSPFLLDKFQQQLESKKTEPEHRPMSSIFFDAGSKASLPPCCGQASTPLSSMGGRSNTQWPPDPPLHFG
      PTKWAVGDQRTEFLGAAPLG-----PPVSPPHVSTFKTRSAKGFGARGPDVLSPAMVALSNKLKLKRQLEYE
      EQAFQDLSGGDPPGGSTSHLMWKRMKNLRGGSCPLMPDKPLSANVPNDKFTQNPMRGLGHPLRHLPLPQPPS
      AISPGENSKSRFPPQCYATQYQDYSLSSAHKVSGMASRLLGPSFESYLLPELTRYDCEVNVPVLGSSTLLQG
      GDLLRALDQAT

      3d-beacons now has a Levylab source providing oligomeric alphafold based structures - these should be ranked in the same way as alphafold and imported with alphafold quality scores.

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: