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nav-list wwpdb-sidenav'> <li class='menu-title'>Archive Downloads</li> <li ><a href='/ftp/pdb-ftp-sites' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB Archive</a></li> <li ><a href='/ftp/pdb-versioned-ftp-site' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB Versioned Archive</a></li> <li class='active'><a href='/ftp/pdb-nextgen-archive-site' ><i class='glyphicon glyphicon-chevron-right' style='color:#888'></i> PDB NextGen Archive </a></li> </ul> </div> <div class="col-md-9"> <div class="wwpdb-content"> <!-- BEGIN CONTENT--> <style> pre { white-space: pre-wrap; /* Since CSS 2.1 */ white-space: -moz-pre-wrap; /* Mozilla, since 1999 */ white-space: -pre-wrap; /* Opera 4-6 */ white-space: -o-pre-wrap; /* Opera 7 */ /*word-wrap: break-word;*/ /* Internet Explorer 5.5+ */ } </style> <h1>PDB NextGen Archive</h1> <p>Since February 01 2023, the wwPDB enriches PDB entries with additional annotation and distributes the latest versions of each entry via next generation archive (NextGen) accessible at <a href="https://files-nextgen.wwpdb.org/" target="_blank">https://files-nextgen.wwpdb.org</a> and its mirrors in the USA, UK and Japan. </p> <h3 class="underline">PDB NextGen Repository</h3> <p>The PDB NextGen Repositories are updated every month on the 1st Wednesday at 00:00 UTC.</p> <p>wwPDB: <a href="https://files-nextgen.wwpdb.org" target="_blank">https://files-nextgen.wwpdb.org</a>, rsync://rsync-nextgen.wwpdb.org <br /> RCSB PDB (USA): <a href="https://files-nextgen.rcsb.org" target="_blank">https://files-nextgen.rcsb.org</a>, rsync://rsync-nextgen.rcsb.org<br /> PDBe (UK): <a href="https://ftp.ebi.ac.uk/pub/databases/pdb_nextgen/" target="_blank">https://ftp.ebi.ac.uk/pub/databases/pdb_nextgen/</a><br /> PDBj (Japan): <a href="https://files-nextgen.pdbj.org" target="_blank">https://files-nextgen.pdbj.org</a>, rsync://rsync-nextgen.pdbj.org </p> <h3 class="underline">What is Enriched in the PDB Entry </h3> <p>This 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For example, the sequence annotation from external resources such as UniProt, SCOP2 and Pfam are provided at atom, residue, and chain levels: _pdbx_sifts_unp_segments and _pdbx_sifts_xref_db_segments for each segment, _pdbx_sifts_xref_db at residue level, and _atom_site at the atom level.</p> <p>More external annotation will be added as this archive grows.</p> <h3 class="underline">Directory structure of the PDB NextGen archive</h3> <p>This archive uses the extended PDB accession codes to 8 characters prefixed with “pdb” in file naming, e.g., "pdb_00001abc"</p> <p>Similar to the versioned PDB archive, in the NextGen tree all files for a particular entry are stored in single directory (e.g., "pdb_00001abc").</p> <p>These directories are grouped under a 2-character hash from the two penultimate characters of the PDB code (last character minus 2 and last character minus 1). For example, the hash would be "ab" for PDB entry "pdb_00001abc"):</p> <p><pre>../pdb_nextgen/data/entries/divided/&lt;two-letter-hash&gt;/&lt;pdb_accession_code&gt;/&lt;entry_data_File_names&gt;</pre></p> <p>Thus, all files for entry pdb_00001abc would be stored in the following directory:</p> <p><pre>../pdb_nextgen/data/entries/divided/ab/pdb_00001abc/</pre></p> <h3 class="underline">File names in the NextGen archive</h3> <p>File names in the NextGen archive conform to a similar naming scheme as versioned archive with a tag “enrich” to identify the source of PDB archives:</p> <p><pre>&lt;PDB_ID>_&lt;content_type&gt;-&lt;archive resource&gt;.&lt;file_format_type&gt;.&lt;file_compression_type&gt;</pre></p> <p>For example, the latest version of PDB entry 1abc would have the following form under the new file-naming scheme:</p> <p><pre>pdb_00001abc_xyz-enrich.cif.gz</pre></p> <p><pre>pdb_00001abc_xyz-no-atom-enrich.xml.gz</pre></p> <!-- END CONTENT--> </div> </div> </div> <br> <footer 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