The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal-organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
We report the generation and characterization of the most complete collection of metal-organic frameworks (MOFs) maintained and updated, for the first time, by the Cambridge Crystallographic Data Centre (CCDC). To set up this subset, we asked the question "what is a MOF?" and implemented a number of "look-for-MOF" criteria embedded within a bespoke Cambridge Structural Database (CSD) Python API workflow to identify and extract information of 69,666 MOF materials. The CSD MOF subset is updated regularly with subsequent MOF additions to the CSD, bringing a unique record for all researchers working in the area of porous materials around the world, whether to perform high-throughput computational screening for materials discovery or to have a global view over the existing structures in a single resource. Using this resource, we then developed and used an array of computational tools to remove residual solvent molecules from the framework pores of all the MOFs identified and went on to analyze geometrical and physical properties of non-disordered structures.
Summary
Crystallographic studies of ligands bound to biological macromolecules (proteins and nucleic acids) represent an important source of information concerning drug-target interactions, providing atomic level insights into the physical chemistry of complex formation between macromolecules and ligands. Of the more than 115,000 entries extant in the Protein Data Bank archive, ~75% include at least one non-polymeric ligand. Ligand geometrical and stereochemical quality, the suitability of ligand models for in silico drug discovery/design, and the goodness-of-fit of ligand models to electron density maps vary widely across the archive. We describe the proceedings and conclusions from the first Worldwide Protein Data Bank/Cambridge Crystallographic Data Centre/Drug Design Data Resource (wwPDB/CCDC/D3R) Ligand Validation Workshop held at the Research Collaboratory for Structural Bioinformatics at Rutgers University on July 30–31, 2015. Experts in protein crystallography from academe and industry came together with non-profit and for-profit software providers for crystallography and with experts in computational chemistry and data archiving to discuss and make recommendations on best practices, as framed by a series of questions central to structural studies of macromolecule-ligand complexes. What data concerning bound ligands should be archived in the Protein Data Bank? How should the ligands be best represented? How should structural models of macromolecule-ligand complexes be validated? What supplementary information should accompany publications of structural studies of biological macromolecules? Consensus recommendations on best practices developed in response to each of these questions are provided, together with some details regarding implementation. Important issues addressed but not resolved at the workshop are also enumerated.
Suzanna Ward and Ghazala Sadiq introduce the CrystEngComm themed issue on the Cambridge Structural Database – a wealth of knowledge gained from a million structures.
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