{
 "id": "protein-data-bank",
 "name": "Protein Data Bank",
 "category": "other",
 "identifiers": {
  "extensions": [
   "pdb",
   "ent",
   "brk"
  ],
  "puid": [
   "fmt/2009"
  ],
  "wikidata": [
   "Q7251429",
   "Q128035062"
  ],
  "mime": [
   "chemical/x-pdb"
  ],
  "signatures": [
   {
    "name": "Protein Data Bank File v.3.3",
    "sequences": [
     {
      "position": "eof",
      "offset": 0,
      "max_offset": 1,
      "pattern": "0a4d4153544552{74-75}0a454e44{77-78}0a"
     },
     {
      "position": "bof",
      "offset": 0,
      "max_offset": 1,
      "pattern": "484541444552{74-80}0a5449544c45{74-250}0a434f4d504e44*0a534f55524345*0a4b4559574453*0a455850445441{74-76}0a415554484f52*0a524556444154*0a52454d41524b*0a435259535431*0a4f5249475831*0a5343414c4531"
     }
    ]
   }
  ]
 },
 "status": "writable",
 "summary": "The Protein Data Bank file format was developed as a human readable, standardised way to describe the 3D structures of molecules. The file is limited to 80 columns, which was based on the width of the computer punch cards that were previously used to exchange the coordinates. It was developed in 1972, and has gone through various versions, the last one being version 3.3 (defined here), which was released in 2012. The file was succeeded by the .mmCIF format in 2014.",
 "projects": [
  {
   "name": "File Formats Wiki",
   "url": "http://fileformats.archiveteam.org/wiki/Protein_Data_Bank",
   "kind": "wiki"
  },
  {
   "name": "PRONOM fmt/2009",
   "url": "https://www.nationalarchives.gov.uk/PRONOM/fmt/2009",
   "kind": "format-doc"
  },
  {
   "name": "Wikidata Q7251429",
   "url": "https://www.wikidata.org/wiki/Q7251429",
   "kind": "wiki"
  },
  {
   "name": "Wikidata Q128035062",
   "url": "https://www.wikidata.org/wiki/Q128035062",
   "kind": "wiki"
  }
 ],
 "provenance": {
  "sources": [
   "converters",
   "ffw",
   "pronom",
   "wikidata"
  ]
 },
 "updated": "2026-10-24",
 "tools": [
  {
   "name": "ImageMagick",
   "url": "https://imagemagick.org",
   "license": "ImageMagick License",
   "open_source": true,
   "reads": true,
   "writes": true
  },
  {
   "name": "Abalone",
   "url": "http://www.biomolecular-modeling.com/Abalone/",
   "reads": true,
   "writes": true,
   "license": "proprietary license"
  },
  {
   "name": "Amira",
   "url": "http://www.amira.com",
   "reads": true,
   "writes": false
  },
  {
   "name": "Avogadro",
   "url": "https://avogadro.cc/",
   "reads": true,
   "writes": false,
   "license": "3-clause BSD License",
   "open_source": true
  },
  {
   "name": "BALL",
   "url": "http://www.ball-project.org/",
   "reads": true,
   "writes": false,
   "license": "GNU Lesser General Public License",
   "open_source": true
  },
  {
   "name": "bioSyntax",
   "url": "http://bioSyntax.org",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License, version 3.0",
   "open_source": true
  },
  {
   "name": "BIOVIA Discovery Studio",
   "url": "https://www.3ds.com/products/biovia/discovery-studio",
   "reads": true,
   "writes": false
  },
  {
   "name": "Blender",
   "url": "https://www.blender.org",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License, version 3.0",
   "open_source": true
  },
  {
   "name": "CASTp",
   "url": "http://sts-fw.bioengr.uic.edu/castp/index.php",
   "reads": true,
   "writes": false
  },
  {
   "name": "Chem3D",
   "url": "https://www.wikidata.org/wiki/Q114131678",
   "reads": true,
   "writes": false
  },
  {
   "name": "Cn3D",
   "url": "https://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3d.shtml",
   "reads": true,
   "writes": false,
   "license": "public-domain software",
   "open_source": true
  },
  {
   "name": "Coot",
   "url": "https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License",
   "open_source": true
  },
  {
   "name": "Gabedit",
   "url": "http://gabedit.sourceforge.net/",
   "reads": true,
   "writes": false,
   "license": "X11 license",
   "open_source": true
  },
  {
   "name": "GeNMR",
   "url": "http://www.genmr.ca/index.php",
   "reads": false,
   "writes": true
  },
  {
   "name": "GENtle",
   "url": "https://www.wikidata.org/wiki/Q5513179",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License, version 2.0 or later",
   "open_source": true
  },
  {
   "name": "Geworkbench",
   "url": "http://www.geworkbench.org",
   "reads": true,
   "writes": false,
   "license": "open-source license",
   "open_source": true
  },
  {
   "name": "iCn3D",
   "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html",
   "reads": true,
   "writes": false
  },
  {
   "name": "Jmol",
   "url": "http://jmol.sourceforge.net/",
   "reads": true,
   "writes": false,
   "license": "GNU Lesser General Public License",
   "open_source": true
  },
  {
   "name": "Molconvert",
   "url": "https://chemaxon.com/products/marvin",
   "reads": true,
   "writes": false
  },
  {
   "name": "Molden",
   "url": "http://cheminf.cmbi.ru.nl/molden/",
   "reads": true,
   "writes": false
  },
  {
   "name": "Molekel",
   "url": "https://ugovaretto.github.io/molekel/",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License",
   "open_source": true
  },
  {
   "name": "NAMD",
   "url": "http://www.ks.uiuc.edu/Research/namd",
   "reads": true,
   "writes": false
  },
  {
   "name": "Nugraf",
   "url": "https://www.wikidata.org/wiki/Q113044711",
   "reads": true,
   "writes": false
  },
  {
   "name": "OpenBabel",
   "url": "https://openbabel.org",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License, version 2.0 or later",
   "open_source": true
  },
  {
   "name": "PolyTrans 4.1.2",
   "url": "https://www.okino.com/conv/conv.htm",
   "reads": true,
   "writes": false
  },
  {
   "name": "PyMOL",
   "url": "http://pymol.org/",
   "reads": true,
   "writes": false,
   "license": "source available license"
  },
  {
   "name": "Q1036510",
   "url": "https://biojava.org/",
   "reads": true,
   "writes": false,
   "license": "GNU Lesser General Public License",
   "open_source": true
  },
  {
   "name": "RasMol",
   "url": "http://www.rasmol.org/",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License",
   "open_source": true
  },
  {
   "name": "RASMOL",
   "url": "https://www.wikidata.org/wiki/Q128889946",
   "reads": true,
   "writes": false
  },
  {
   "name": "UCSF Chimera",
   "url": "http://www.cgl.ucsf.edu/chimera/index.html",
   "reads": true,
   "writes": false
  },
  {
   "name": "UGENE",
   "url": "http://ugene.net",
   "reads": true,
   "writes": false,
   "license": "GNU General Public License",
   "open_source": true
  },
  {
   "name": "VisIt",
   "url": "http://visit.llnl.gov/",
   "reads": true,
   "writes": false,
   "license": "BSD licenses",
   "open_source": true
  },
  {
   "name": "Visual Molecular Dynamics",
   "url": "http://www.ks.uiuc.edu/Research/vmd/",
   "reads": true,
   "writes": false
  },
  {
   "name": "WHAT IF software",
   "url": "http://swift.cmbi.ru.nl/whatif",
   "reads": true,
   "writes": false
  },
  {
   "name": "Yasara",
   "url": "http://www.yasara.org",
   "reads": true,
   "writes": false,
   "license": "proprietary license"
  }
 ],
 "version": "3.3",
 "conversions": [
  {
   "to": "portable-network-graphics",
   "tool": "ImageMagick",
   "command": "convert in.pdb out.png",
   "fidelity": "lossless",
   "losses": "Pixels kept; some metadata, colour profiles or layers may be dropped.",
   "url": "https://imagemagick.org"
  },
  {
   "to": "tagged-image-file-format",
   "tool": "ImageMagick",
   "command": "convert in.pdb out.tif",
   "fidelity": "lossless",
   "losses": "Pixels kept; some metadata, colour profiles or layers may be dropped.",
   "url": "https://imagemagick.org"
  },
  {
   "to": "jpeg-file-interchange-format-1-02",
   "tool": "ImageMagick",
   "command": "convert in.pdb out.jpg",
   "fidelity": "lossy",
   "losses": "Lossy compression.",
   "url": "https://imagemagick.org"
  },
  {
   "to": "webp",
   "tool": "ImageMagick",
   "command": "convert in.pdb out.webp",
   "fidelity": "lossy",
   "losses": "Lossy compression.",
   "url": "https://imagemagick.org"
  },
  {
   "to": "gif",
   "tool": "ImageMagick",
   "command": "convert in.pdb out.gif",
   "fidelity": "lossy",
   "losses": "Reduced to 256 colours.",
   "url": "https://imagemagick.org"
  }
 ],
 "aliases": [],
 "structure": [],
 "parsers": [],
 "samples": [],
 "claims": [],
 "verification": []
}