Macromolecule Hub
Macromolecule Hub — Mine the World’s Structural Science Knowledge from the PDB and CSD in One Secure, Online Platform
Access data from the Protein Data Bank, the Cambridge Structural Database, and your in-house database(s).
Perform advanced searching across protein-ligand binding sites and small molecule structures, including 2D and 3D search. Propose changes to your drug structure based on observations from real-world findings in the PDB and CSD. Understand how the interactions, conformations, and behaviour you observe for a given target-ligand pair compares to existing observed systems.
Features
Secure, web-based access
No local installation required, simply go to the URL to begin. The system is set up on-site, safely behind your company firewall, so your work is secure.
Mine insights across binding site and ligand structures
Perform 2D and 3D searches for specific motifs observed in binding sites, ligands, or both. Use these to develop your drug structure, suggest modifications or understand interactions and conformations.
Brings chemistry and biology data together
Search PDB and CSD data with one tool — the world’s trusted sources of experimentally observed small molecule and macromolecular data. No need to learn different interfaces and systems.
2D & 3D substructure search
Flexible searching, with ability to mine interaction or conformation data.
Share findings easily
Share your results with your colleagues simply by sending them the URL link.
Single source for 3D crystallographic data
Search and mine crystallography data from the major data sources, the CSD and PDB, in one system.
Included in
Fields
Use Cases
Search and Mine Protein Binding Site Data in One Secure, Online Platform
Watch this 2-minute video to learn how the Macromolecule Hub can help you to:
- Access data from the Protein Data Bank, the Cambridge Structural Database, and your in-house database(s).
- Perform advanced searching across protein-ligand binding sites and small molecule structures, including 2D and 3D search.
- Propose changes to your drug structure based on observations from real-world findings in the PDB and CSD.
- Understand how the interactions, conformations, and behaviour you observe for a given target-ligand pair compares to existing observed systems.
FAQs
Currently the ligated protein-ligand binding sites of all PDB structures are included. If a protein has more than one binding site, all which have a ligand-bound structure published will be included.
Observed pockets that do not have a ligand in them are not currently included, nor are the rest of the protein structure outside of the binding site. This choice was made so you can focus in on active sites.
At the moment, only the Cambridge Structural Database (CSD) and Protein Data Bank (PDB) binding sites are included. There are plans to develop the system further in the future, with the potential to add other data sources including proprietary data. If this is of interest do get in touch here and we can keep you informed of developments.
Yes — you can perform 2D and 3D searching, and search by planes, torsions, vectors just like in ConQuest. This is all done via a web-based interface, so you don’t need a local install, and neither do your colleagues; share results by simply sharing the URL to them.
Yes — the system is set up behind your company firewall in an on-site instance, so any searches you perform are secure and private.
Our former product Relibase was retired in 2018 and offered similar functions, but Macromolecule Hub has a host of improvements vs Relibase. It allows CSD and PDB data to be accessed in one platform, and is accessible via a URL with no local install required. It is still installed behind your company firewall, for secure work.