Good news for you small molecule structure enthusiasts – the Cambridge Structural Database (CSD, or CSD System – CSDS) – is now available on Linux servers supported by Research Computing, as well as through the web and through CSDS client software.
For those not familiar with the CSDS, it’s the principal repository for crystal structure information for over 500,000 organic and metal-organic compounds. Structure data is drawn from the chemical literature and is also added to the CSD via direct deposit by researchers. The CSD is maintained by the Cambridge Crystallographic Data Center.
The whole CSD system comprises the CSD along with an integrated suite of software tools for database access and information retrieval, structure visualisation and data analysis, and structural knowledge bases derived from the CSD (e.g. IsoStar, a knowledge base of intermolecular interactions containing data derived from both the CSD and the PDB).
The Library provides access to the CSD in multiple ways:
- There’s a web version – WebCSD – available to Dartmouth users on the campus network or connected through VPN. Though lacking some of the high-powered capabilities of the desktop software and the Linux versions, the web version allows similarity and substructure searching, as well as searching by bibliographic (journal citation) information and by compound name and other text and numerical fields.
- CSD desktop software for Windows and Mac – this software is available for Dartmouth users to install on their workstations for convenient and powerful CSD access. The DVDs are on reserve at the Kresge Library circulation desk, and you can check them out for 24 hours to install the software. The desktop software version includes the full suite of software tools referenced above.
- Finally and most recently, The CSDS tools are available to Research Computing accounts on the Polaris and Andes Linux servers. Users should run “module load csds” to make the software available. Other Linux systems with AFS client software should be able to run the software without needing to install it locally. Consult Research Computing for assistance with setting this up.
More CSDS links and information:
- release & installation notes
- user guides and tutorials for each of the components of the CSD system (ConQuest, Mercury, VISTA and others)
- a set of worked examples that illustrate application uses of other specialized software components (Mogul, Materials Mercury and Isostar)
CCDC – Case Studies
From both the Life Sciences and Small Molecule research areas (examples Assessing the reliability of protein-ligand structures, or Assessing the likelihood of polymorphism through Hydrogen bond capabilities)
Using the CSD For Teaching
Presentations from a symposium at the 2009 ACS National Meeting in Washington DC (examples “Bond lengths, crystal structure determinations, and research in the undergraduate classroom”; “Using the Cambridge Structural Database to explore concepts of symmetry”)
CCDC – Useful Links
Software tools, computational chemistry, modelling software, major databases and repositories, crystallographic associations