**
*Dear all,*
*
We’re excited to announce the release of PDBe’s new Ligand Pages, a
significant upgrade to the PDBeChem service! This revamped platform
introduces many new features and offers a more comprehensive and
user-friendly way to explore small molecule data in the Protein Data
Bank (PDB).
Key features of these new Ligand Pages:
1.
Enhanced Ligand Descriptions: Includes detailed molecular
information, visualisations (2D/3D), physicochemical properties, and
substructures like Murcko scaffolds and ligand fragments.
2.
Bound Structures Overview: Provides aggregated protein and
individual PDB data, detailing protein name, source organism, ligand
functional roles, and more.
3.
Interaction Statistics: aggregates atom-level interaction data
between ligands and proteins in PDB, visualised through heatmaps and
2D ligand diagrams to identify hotspots and interaction patterns.
4.
Related Ligands: Highlights structurally similar ligands grouped by
same scaffold, ≥60% similarity, stereoisomers, shown in an image
gallery with further details.
5.
Cross-links to Other Databases: Integrates with external resources
like ChEMBL, PubChem, KEGG, DrugBank, and others for seamless
exploration.
These updates provide a unified view of ligand data in PDB, enabling
researchers to investigate ligand interactions and their biological
significance more effectively.
Explore these new ligand pages
*
Check out the updated Ligand Page for Imatinib (CCD ID: STI):
pdbe.org/chem/sti <pdbe.org/chem/sti>
*
Access the user tutorial for a step-by-step guide: PDBe Ligand Pages
Tutorial
<https://github.com/PDBeurope/pdbe-notebooks/blob/main/pdbe_ligands_tutorials/PDBe_PDBe-KB_ligands_webpages_tutorials.pdf>
For full details on this new release, read the full
announcementhere:https://www.ebi.ac.uk/pdbe/news/pdbe-team-introduces-novel-ligand-pages-revamped-pdbechem-service
<https://www.ebi.ac.uk/pdbe/news/pdbe-team-introduces-novel-ligand-pages-revamped-pdbechem-service>.
If you have any questions or need assistance, please feel free to reach
out to us at pdbeh...@ebi.ac.uk <mailto:pdbeh...@ebi.ac.uk>.
We hope you’ll find this new resource useful in your research!
Kind regards,
Deborah Harrus, on behalf of 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
-------------------------------------------------------------------
########################################################################
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/
