**
*We have updated the tools used at PDBe and PDBe-KB for processing small
molecule ligands and their interactions in the PDB archive. This process
now identifies larger, linked ligands that are composed of individual
components covalently linked together, allowing these molecules to be
identified in a standardised manner for the first time.*
*
The ‘pdbeccdutils’ python library
(https://github.com/PDBeurope/ccdutils) has been developed for the
processing of small molecules in the PDB and this update sees a number
of improvements to the pipeline. This process is used to generate data
in PDBe’s updated CCD files, including standard 2D and 3D depictions,
fragment and scaffold identification, external database mapping, and more.
The updates to pdbeccdutils includes the addition of a new module to
determine ‘bound molecules’, defined as multiple, covalently linked CCD
ligands into a single, larger molecule. There are also updates to the
underlying packages, including use of RDKit 2022.09.x for generating
molecular properties, and use of Gemmi for parsing PDBx/mmCIF format
files. There is one breaking change, which is the replacement of
ccd_cif_dict with ccd_cif_block in the updated CCD files.
There have also been updates to PDBe Arpeggio, our version of Arpeggio,
a python library originally developed by the Blundell group. The PDBe
Arpeggio python library generates interactions data for proteins and
ligands in the PDB archive. This update to v1.5 includes improvements in
identification of different molecule types and updates to underlying
packages, including Open Babel v3.0.0 and inclusion of Gemmi for parsing
PDBx/mmCIF files.
For more information about the updates to pdbeccdutils and PDBe
Arpeggio, view the full news item at
https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe
<https://www.ebi.ac.uk/pdbe/news/updated-pipeline-small-molecule-data-processing-pdbe>
Kind Regards,
David Armstrong
*
--
David Armstrong
Outreach and Training Lead
PDBe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
########################################################################
To unsubscribe from the CCP4BB list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list
hosted by www.jiscmail.ac.uk, terms & conditions are available at
https://www.jiscmail.ac.uk/policyandsecurity/
