Cambridge Structural Database - 2018 version available | Stanford Libraries

Cambridge Structural Database - 2018 version available

February 8, 2018
Grace Baysinger

CSD Refcode TUWMOP - the 800,000th entry added to the CSD

Established in 1965 by the Cambridge Crystallographic Data Centre (CCDC), the Cambridge Structural Database (CSD) is the world’s repository for small-molecule organic and metal-organic crystal structures. Containing over 900,000 entries from x-ray and neutron diffraction analyses, this unique database of accurate 3D structures has become an essential resource to scientists around the world.  The June 2015 issue of CCDC's Crystalline Newsletter covers 50 Years of Sharing Crystal Structures (PDF).  In addition to coverage of the published literature, CSD searches also contains data published directly through the CSD as CSD Communications that are not available anywhere else. 

We have a campus-wide site license for CSD Enterprise which includes all CSD software and all application data (see Components).  Software modules include everything in the CSD-SystemCSD-Discovery (plus CSD-CrossMiner), and CSD-Materials.  Download the latest version and get license keys.

The Cambridge Structural Database 2018: What’s New? (PDF) provides a summary.  Below are more details. 

What's new for the CSD-System in 2018?

  • This year they introduced a new suite of features in Mercury to help you visualize, understand and modify the symmetry of crystal structures including the ability to:
    • View along unit cell or Miller directions
    • Link directly to International Tables for Crystallography Volume A (Space-group symmetry) online
    • Reduce symmetry from the current space group to any valid subgroup
  • During 2017, they also introduced a new version of WebCSD (v2) which is:
    • Fully cross-platform – for desktop, tablet and mobile
    • Current – with up-to-the-minute data updates
    • Searchable – by 2D structure, unit cell and text/numeric fields
  • Further enhancements to the CSD-System software include:
    • Improved searching in ConQuest, including more effective reduced cell search
    • Improved handling of bridged rings in Mogul
    • A new contact group in IsoStar – organic iodine

For more information, please see About CSD-System, CSD-System Brochure (PDF), CSD Product Datasheet, CSD-System Components,

What's New for CSD-Discovery in 2018

  • This year they introduced the new application CSD-CrossMiner – an interactive and highly versatile pharmacophore query tool. CSD-CrossMiner is provided with ready-to-use databases for navigating both the CSD and protein-ligand binding sites from the PDB. This delivers an overall interactive search experience with application areas including interaction searching, scaffold hopping and the identification of novel fragments for specific protein environments.
  • Other improvements made to CSD-Discovery include:
    • Improvements to CSD Conformer Generator to better account for sparse distributions and rarer ring conformations
    • A new CSD Python API menu in Hermes allowing you to create and run your own Python scripts within the Hermes application
    • Cavity viewing and highlighting of proteins
    • Improvements to GOLD for configuration of constraints
    • Exposure of pharmacophoric-driven constraints for docking

CSD-Discovery Future Developments

  • Fragment Hotspot Maps
    • Identify fragment binding sites on an apo protein
  • Pocket Search
    • Ultrafast binding site comparison methodology

For more information, see About CSD-Discovery, CSD-Discovery Components, About CrossMiner

What’s new for CSD-Materials in 2018?

  • They have improved DASH, their application for structure solution from PXRD data, to solve crystal structures faster and more consistently. New, more effective, simulated annealing parameters have been introduced to DASH resulting from a focused research study in collaboration with the University of Reading.
  • Additional enhancements made to the CSD-Materials components include
    • Streamlining of the Hydrogen-Bond Propensity (HBP) wizard for improved usability
    • New bromine & iodine probes added to Full Interaction Maps to analyze halogen-bonding interactions

For more information, see: About CSD-Materials, CSD-Materials Brochure (PDF), CSD-Materials Components

Examples of visualizations you can do with CSD-Discovery and CSD-Materials are shown below.

CSD-Discovery module images   CSD-Materials module images

 

accessibilityaccessprivsarrow-circle-rightaskus-chataskus-librarianbarsblogsclosecoffeecomputercomputersulcontactsconversationcopierelectricaloutleteventsexternal-linkfacebook-circlegroupstudyhoursindividualinterlibrarynewsnextoffcampusopenlateoutdoorpeoplepolicypreviousprinterprojectsquietreservesscannersearchstudysupportingtabletourstwitter-circleworking