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Chemistry and Chemical Engineering: Cambridge Structural Database - Trial

Introduce data and information resources in Chemistry, Chemical Engineering, and related fields for Mines community.

Cambridge Structural Database

ccdc logoCambridge Structural Database (CSD) is a world wide repository of small-molecule organic and metal-organic crystal structure hosted by Cambridge Crystallographic Data Center (CCDC). Colorado School of Mines now has a trial access to the CSD 2017. Please send any feedback about CSD to yeli@mines.edu or aseiffert@mines.edu.

Access to Cambridge Structural Database

Affiliates of Colorado School of Mines can access the database via either of the following means.

  1. WebCSD - http://webcsd.ccdc.cam.ac.uk

    • If you are off campus, please turn on your Mines VPN connection to ensure access.
    • Requires Java. Use Internet Explorer V6 or later OR Safari V4 or later to access. See more at this link.
    • Only use WebCSD for quick search and browsing since 3D structure search, advanced similarity search, molecular geometry validation, and molecule interactions are not available on WebCSD interface.
  2. Install Cambridge Structural Database System (CSDS) on your own computer

    • Request links to download the software at: http://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/. You will need our site number/confirmation code (Email yeli@mines.edu to request) and your username@mines.edu email address. Once you submit the request successfully, an email with the download links will be sent to you. (Be sure to check your Spam folder.) Follow the links and instructions in the email to download and install the software appropriate to your operating system.
    • You will need the Site No. and Confirmation Code again to register for the system after it is installed. Start Mercury or ConQuest or Mogul to register.  Please read the release_install.pdf document after you download the software for troubleshooting problems during installation.

Components of CSD

Mines affiliates have access to CSD-Enterprise 2017, including CSD-System, CSD-Discovery, and CSD-Materials. The summary of functions of each suite is excerpted from CCDC website and listed below. You can use the software suite to explore over 840,000 entries of fully validated crystal structures and also to analyze intra- and intermolecular interactions to understand structure-property / structure - behavior relationships. Meanwhile, the Python API tools will allow you to query the database easily and integrate data with your current workflow.

 

CSD-System Applications

  • Find structures with WebCSD
    • Cross-platform web-based structure lookup for the research community
  • Search with ConQuest
    • Answer very specific structure questions on your desktop using highly flexible 3D searching of the CSD and local in-house databases
    • Quickly identify structures based on a wide range of properties
    • Use interaction and structure-property knowledge to drive design decisions
  • Visualise and analyse in Mercury
    • Represent molecular conformations, crystal structures, crystallographic planes and simulated morphologies with high quality graphics and videos
    • 3D print your molecules and structures
  • Conformations using Mogul
    • Harness the millions of chemically classified bond lengths, angles, torsion angles, and ring conformations in the CSD to obtain precise information on preferred molecular geometries
  • Interactions with IsoStar
    • Use the wealth of interaction information available in the CSD and in the Protein Data Bank (PDB) to show the probability and characteristics of interactions between specific pairs of chemical functional groups
  • Connect with the CSD Python API (Application Programming Interface)
    • Create tailored scripts using the whole spectrum of CSD functionality to answer your targeted research questions
    • Integrate access to crystal data and CSD functions seamlessly with 3rd party software

CSD-Discovery Applications

  • Docking
    • Perform protein-ligand docking experiments and virtual screening using GOLD
       
  • Geometry
    • Validate your receptor-bound ligand geometry using the same CSD routines in place at the Protein Data Bank
    • Drive the design of your ligands by knowledge driven prediction of their geometry
    • Generate conformers derived directly from all the latest validated experimental data from the CSD
  • Interactions
  • Virtual Screening
  • Access
    • Create, or download from our portal, CSD-driven analyses and workflows. Publish them to your own menu in Mercury with the CSD Python API

CSD-Materials Applications

  • Explore with Mercury
    • Discover preferred intra- and intermolecular interactions and engineer changes to satisfy these requirements using Full Interaciton Maps
    • Interpret crystal packing and compare with CSD data using powerful packing feature, similarity and motif searches, and hydrogen bond propensity analysis
    • Understand the effects of hydration on your lattice with the new hydrate analyser
    • Explore the structures of potential co-crystals using the new molecular complementarity tool
    • Explore solid state molecular geometry using the new CSD-driven Conformer Generator – unique because all results are validated by all the latest experimental data from the CSD
    • Communicate your results with new high impact graphics and 3D printing support, highlighting lattice void spaces and channels
  • Determine structures with DASH
    • Solve your powder crystal structure using CSD data
  • Connect with the CSD Python API (Application Programming Interface)
    • Create, or download from our portal, CSD-driven analyses and workflows. Publish them to your own menu in Mercury

 

Learn More about CSD

CSD contains over 840,000 x-ray and neutron diffraction analysis. It provides 3D structures with respective coverage of the published literature. The structural data is curated and enriched with bibliographic, chemical and physical property information. More than 40,000 new structures are added to the database each year. The database is useful for Crystallography, Structure-based drug design, Medicinal chemistry, Pharmaceutical formulation and development, Material science, and Education.

CCDC provides: