<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class=""><p class="">A new data representation for carbohydrates in PDB entries and
reference data improves the Findability and Interoperability of these
molecules in macromolecular structures. The PDB archive now reflects:</p><ul class=""><li class=""> Standardized Chemical Component Dictionary nomenclature following IUPAC-IUBMB recommendations</li><li class=""> Uniform representation for oligosaccharides</li><li class=""> Adoption of glycoscience-community commonly used linear descriptors using community tools</li><li class=""> Annotated glycosylation sites in PDB structures</li></ul></div><div class=""><p class="">Detailed information about this project, including a list of remediated PDB entries, is available at the <a href="https://www.wwpdb.org/documentation/carbohydrate-remediation" class="">wwPDB website</a>.
Developers of software packages that produce, access, or visualize PDB
data are encouraged to review this information and adapt their software
as soon as possible, as originally highlighted in the <a href="https://www.wwpdb.org/news/news?year=2020#5e53e52f2d410731e9944f40" class="">February 2020 announcement</a>.</p><p class="">The
wwPDB has created a new ‘branched’ entity representation for
polysaccharides, describing all the individual monosaccharide components
of these in the PDB entry. As part of this process, we have
standardized atom nomenclature of >1,000 monosaccharides in the
Chemical Component Dictionary (CCD) and applied a branched entity
representation to oligosaccharides (>8,000 PDB entries). To guarantee
unambiguous chemical description of oligosaccharides in the affected
PDB entries, an explicit description of covalent linkage information
between their monosaccharide units is included. In addition, wwPDB
validation reports provide consistent representation for these
oligosaccharides and include 2D representations based on the Symbol
Nomenclature for Glycans (SNFG).</p><p class="">To support the remediation of
carbohydrate representation, software tools providing linear descriptors
were developed in collaboration with the glycoscience community to
enable easy translation of PDB data to other representations commonly
used by glycobiologists. These include Condense IUPAC from <a href="https://urldefense.com/v3/__https://github.com/GLYCAM-Web/gmml__;!!Mih3wA!X2S8r7MdhdUC1L454I4SaSok4PUaYfAqTrGRViyKDaGbVmfExYkZwoP9vGiF_Oio8g$" class="">GMML</a> at University of Georgia, <a href="https://urldefense.com/v3/__https://gitlab.com/glyconavi/pdb2glycan__;!!Mih3wA!X2S8r7MdhdUC1L454I4SaSok4PUaYfAqTrGRViyKDaGbVmfExYkZwoP9vGjH1sKKEA$" class="">WURCS</a> from PDB2Glycan at The Noguchi Institute, Japan, and <a href="https://urldefense.com/v3/__http://www.glycosciences.de/tools/pdb2linucs/__;!!Mih3wA!X2S8r7MdhdUC1L454I4SaSok4PUaYfAqTrGRViyKDaGbVmfExYkZwoP9vGhOT7W8gA$" class="">LINUCS</a> from pdb-care at Germany.</p><p class="">wwPDB has also used this opportunity to improve the organization of chemical synonyms in the CCD by introducing a new <tt class="">_pdbx_chem_comp_synonyms</tt>
data category. This will enable more comprehensive capture of
alternative names for small molecules in the PDB. To minimize disruption
to users, the legacy data item, <tt class="">_chem_comp.pdbx_synonyms</tt>, will be retained for a transition period through 2021.</p><p class="">The carbohydrate remediation project is a wwPDB collaborative project carried out principally by <a href="https://urldefense.com/v3/__http://rcsb.org/__;!!Mih3wA!X2S8r7MdhdUC1L454I4SaSok4PUaYfAqTrGRViyKDaGbVmfExYkZwoP9vGh4wY6etw$" class="">RCSB PDB</a> at Rutgers, The State University of New Jersey and is funded by NIGMS grant U01 CA221216 in collaboration with <a href="https://urldefense.com/v3/__https://www.ccrc.uga.edu/__;!!Mih3wA!X2S8r7MdhdUC1L454I4SaSok4PUaYfAqTrGRViyKDaGbVmfExYkZwoP9vGhn_IGT7g$" class="">Complex Carbohydrate Research Center at the University of Georgia</a>.</p><p class="">If you have any comments or queries regarding these changes, please visit the <a href="https://www.wwpdb.org/documentation/carbohydrate-remediation" class="">wwPDB carbohydrate remediation website</a> or contact us at <a href="mailto:deposit-help@mail.wwpdb.org" class="">deposit-help@mail.wwpdb.org</a>.</p></div><div class=""><br class=""></div><a href="https://www.wwpdb.org/news/news?year=2020#5f17634f0b582626e650e48b" class="">https://www.wwpdb.org/news/news?year=2020#5f17634f0b582626e650e48b</a><div class=""><br class=""></div><div class=""><br class="">
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