CSD-CrossMiner matches molecules to targets through intuitive, interactive data mining.

Build pharmacophore queries and simultaneously mine the CSD, PDB and your proprietary structural data to quickly identify off-target effects, alternative scaffolds, similar binding sites, interaction motifs, bioisosteres and more.

Advance your hit to lead and lead optimisation steps with this deep understanding of interactions in your system of interest.


Intuitive pharmacophore searching

Easily build and modify queries around key pharmacophore features, to search for proteins and ligands the way you see them. Define key features like H-bond acceptors and donors, rings, halogens, and heavy atoms, then find proteins or ligands which match this pattern.

Search your proprietary data

Examine your database in a new way. Mine your in-house structural database with pharmacophore search in CSD-CrossMiner to put the knowledge to work, and even uncover new uses for old structures.

Customise feature definitions

Control your search and explore new chemistry–with custom features to improve search granularity based on your needs.

Interactive user interface

Change your hypothesis on the fly, and get instant results as your search evolves. Immediately understand how each feature impacts your results.

CSD and PDB databases included

Start now–with the key global structural databases for proteins and small molecules already set up.

Excluded volume

Cut the noise by removing occupational volume. This acts like a "NOT" function, to filter results based on your knowledge of the target and binding site. Or use it to explore new areas by blocking those already tested.

Learn more


Case Study: University of Groningen - exploring molecular scaffolds for a synthesized MCR library

Tutorial video: how to build a pharmacophore search in CSD-CrossMiner - watch on YouTube

Tutorial video: how to find scaffold hops with CSD-CrossMiner - watch on YouTube

Origin: CSD-CrossMiner was developed in collaboration with Roche–learn how it was designed in J. Med. Chem.


Can I exclude volume in my structure?

  • Yes–use the excluded volume setting like a "not" function for areas of the target you know are occupied, or to direct your search to alternative areas.

Do I have to save all the results?

  • You can export or save the results returned from any pharmacophore search.

Can I search with boolean logic?

  • No, but you can exclude areas if required.
  • The search is based on pharmacophore features–including hydrogen bond acceptors, heavy atoms, hydrophobes, planar and non-planar rings, halogens, and more.

Can I set constraints?

  • Yes–inter and intra-molecular constraints can be set.

 Can I load the pharmacophore query in other visualisers?

  • Yes–you can export a query in PyMol and view it on other visualisers if required.

 Can results be filtered on the fly?

  • No–you must set the filters before starting, not during the search.
  • However, you can alter the search anytime, with results instantly updating as your search evolves.


See technical FAQs and documents for CSD-CrossMiner


Can't find what you need? Email us–we're happy to help.