Enhanced protein handling and tailored searching

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Written by

Pete Wood

Posted on

May 29, 2019

We are pleased to announce the latest update of the CSD software including enhanced protein handling features throughout the CSD portfolio and greatly improved searching capabilities in the CSD Python API.

We’ve been working hard on improving the protein-handling capabilities across the whole CSD portfolio.

The CSD-CrossMiner feature database has now been expanded to include nucleic acid-containing structures from the PDB. Searching these structures has been augmented by the addition of new, nucleotide specific feature definitions.

There are also new classes in the CSD Python API for nucleic acids and nucleotides as well as new attributes of atoms to handle protein-specific atom information. The latest improvements in the CSD Python API provide the ability to investigate patterns of interactions between protein binding sites, waters, metals and small molecules.

CSD-CrossMiner now includes nucleic acid-containing structures from the PDB.


In the CSD Python API, the searching options have been extended in this release to handle all types of 3D query that are available through ConQuest as well as adding the ability to perform query combinations. This means that 3D objects like centroids, vectors and planes can be constructed and used within scripted substructure searches. Using these new 3D substructure search features it is easy to search for and tabulate, for example, the deviation from planarity of a family of square planar transition metal complexes.

Boolean combinations of queries can also now be used to generate more complex searches. This means it is much easier to construct advanced searches including multiple substructures, or using text/numeric queries as filters. As an example, it is easy to search for structures containing a specific functional group as a query (e.g. ‘sulfonamide’), but also containing known marketed drugs (text search for ‘DRUGBANK’ in the synonym field).

As always, we’re keen to hear your feedback on the latest release as well as what new features or usability improvements to existing features would be most important to you. The CCDC’s software development roadmap is driven by you – our user community. Let us know what you’d like to see featured on our development plan in the next few years.

Peter Wood, CSD-System & CSD-Materials Product Manager


CSD (100)