PDBe Unveils New Streamlined FTP Structure and Enhanced Ligand Data Files

[James Krieger]

We will at some point have to adjust for this. We mostly don't use PDBe but we do have support for it.

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

Or visit the PDBe FTP area directly:
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,
Preeti Choudhary