Dear Frank,
We are indeed harvesting restraints used in refinement, but not
distributing them yet. This should come later this year or early 2025,
and can be made retrospectively.
Kind regards,
Deborah
On 31/01/2024 14:15, Frank von Delft wrote:
Hi Deborah - sounds great, well done!
Are you yet harvesting and serving up the restraints used in
refinement? If not, that remains a huge gap, in my view. (The
chemists tend not to be aware that's even a thing, I keep discovering.)
Frank
On 31/01/2024 13:57, Deborah Harrus wrote:
*Dear all,*
*We're excited to announce significant improvements to ligand data
access and organisation within the PDBe FTP area. These updates aim
to empower your research by simplifying data retrieval and providing
deeper insights into protein-ligand interactions.*
*Key Enhancements:*
*
*Comprehensive Ligand Interaction Data: Two new data files,
Interacting_chains_with_ligand_functions.tsv and
pdb_bound_molecules.tsv, enable large-scale analyses of ligand
interactions across the entire PDB archive including functional
categorisation such as drug-like, reactant-like or cofactor-like.*
*
*Streamlined FTP Directory Structure: The revamped FTP area
features dedicated folders for Chemical Component Definitions
(CCDs), Peptide-like Reference Definitions (PRDs), Covalently
Linked Components (CLCs), and additional data files, facilitating
intuitive data navigation.*
*Benefits for You:*
*
*Perform large-scale ligand interaction analyses across the
entire PDB using complete ligand representations.*
*
*Quick access to all the ligands bound to a specific protein or
identifying all the proteins binding to a specific ligand*
*
*Gain deeper insights into protein function through ligand
interaction and classification.*
*
*Easily access and navigate ligand data with clear file
organisation and unique identifiers.*
*We believe these improvements will enhance ligand data analysis
through streamlined data access and additional functional insights. *
*For more information, visit the PDBe news item
at:https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp
<https://www.ebi.ac.uk/pdbe/news/improved-access-ligand-data-and-annotations-pdbe-ftp>*
*Or visit the PDBe FTP area
directly:https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/
<https://ftp.ebi.ac.uk/pub/databases/msd/pdbechem_v2/>*
*Should you have any questions or require further assistance, please
don't hesitate to contact us.*
*
Sincerely,
Deborah Harrus
The PDBe Team
*
--
-------------------------------------------------------------------
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK
http://www.PDBe.org
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