<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Posted on behalf of my wwPDB colleagues:<div class=""><br class=""></div><div class=""><p class="">In July 2020, the wwPDB will roll out updated PDB structures and
reference data files with standardized representation of carbohydrate
molecules, improving the <i class="">Findability</i> and <i class="">Interoperability</i> of PDB data. <a href="https://www.wwpdb.org/documentation/carbohydrate-remediation" class="">Detailed
information about this work is available from the wwPDB website,
including PDBx/mmCIF dictionary extensions and over 500 example files.</a>
We encourage developers of software packages that produce, access, or
visualize PDB data to review this information and adapt their software.</p><p class="">Through
collaboration with the glycoscience community, software tools were
developed to standardize atom nomenclature of nearly 800 monosaccharides
in the Chemical Component Dictionary (CCD) and applied branched
polymeric representation to oligo- and polysaccharides within the PDB
archive, enabling easy translation to other representations commonly
used by glycobiologists. To guarantee unambiguous chemical description
of oligo-/polysaccharides in each of the nearly 12,000 affected PDB
entries, we have included an explicit description of covalent linkage
information between their monomeric units. To ensure continued <i class="">Findability</i>
of common oligosaccharides (e.g., sucrose, Lewis X factor), we have
expanded the Biologically Interesting molecule Reference Dictionary (<a href="https://www.wwpdb.org/data/bird" class="">BIRD</a>) which will contain the covalent linkage information and common synonyms for such molecules.</p><p class="">wwPDB is also taking this opportunity to improve the organization of chemical synonyms in the CCD by introducing a new <tt class="">_pdbx_chem_comp_synonyms</tt>
data category. This will enable more comprehensive capture of
alternative names for small molecules in the PDB. To minimize disruption
to users, there will be an initial transition period, where the legacy
data item, <tt class="">_chem_comp.pdbx_synonyms</tt>, will be retained.</p><div class=""><br class=""></div><div class="">Source: <a href="https://www.wwpdb.org/news/news?year=2020#5e53e52f2d410731e9944f40" class="">https://www.wwpdb.org/news/news?year=2020#5e53e52f2d410731e9944f40</a></div>
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