Detect epitope amino acids in sequence from BDP file

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    • #117760
      Daniel K
      Participant

      I have a BDP file. It’s id is 4WFF.
      From RCSB website

      Now I have the fasta sequences describing the structures:
      >4WFF_1|Chains A,B|Potassium channel subfamily K member 4|Homo sapiens (9606)
      MTTAPQEPPARPLQAGSGAGPAPGRAMRSTTLLALLALVLLYLVSGALVFRALEQPHEQQAQRELGEVREKFLRAHPCVSDQELGLLIKEVADALGGGADPETQSTSQSSHSAWDLGSAFFFSGTIITTIGYGNVALRTDAGRLFCIFYALVGIPLFGILLAGVGDRLGSSLRHGIGHIEAIFLKWHVPPELVRVLSAMLFLLIGCLLFVLTPTFVFCYMEDWSKLEAIYFVIVTLTTVGFGDYVAGADPRQDSPAYQPLVWFWILLGLAYFASVLTTIGNWLRVVSRRTSNSLEVLFQ
      >4WFF_2|Chains D,F|ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT LIGHT CHAIN|Mus musculus (10090)
      QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMHWYQQKSGTSPKRWIYDTSKLASGVPARFSGSGSGTSYSLTISSMEAEDAATYYCQQWSNSPPTFGAGAKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRN
      >4WFF_3|Chains E,G|ANTI-TRAAK ANTIBODY 13E9 FAB FRAGMENT HEAVY CHAIN|Mus musculus (10090)
      EVQLQQSGPELVKPGASMKTSCKVSGYSFTGYIMNWVKQRHGKNLEWIGLINPNTGYTTYNQKFKGKATLTVDKSSSTAYMELLSLTSEDSAIYYCTRGNYVFDYWGQGTTLTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSSWPSETVTCNVAHPASSTKVDKKIVPRD

      I want to know which part of each sequence is an epitope.
      I tried using IEDB database but with no results.

      Is there any tool or database that can tell the answer?
      I’m not talking about prediction, but on known information.

    • #117765
      Daniel K
      Participant

      I got the PDB file from http://www.rcsb.org/ .

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