Note: Every new release requires a complete re-installation of the software and data.
The latest installation note can be found here (https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/CSD-ReleaseInstallNotes-2020_1.pdf).
The installation takes 3 steps: files download, installation, and entering the license information.
Step 1. File Download
Step 2. Install the Software
Step 3. Enter License Information
Since we recently installed the license server, two options to configure the new install are available to you:
Cambridge Structural Database (CSD) is a worldwide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The latest release is 2020.3.1. The 2020.3 CSD Release contains 1,076,290 unique structures and 1,097,619 entries (CSD version 5.42).
The latest release note can be found here (https://www.ccdc.cam.ac.uk/support-and-resources/ccdcresources/CSD-ReleaseInstallNotes-2020_1.pdf).
The installer contains:
Additionally, we have access to other components that are supplied separately:
See the following web page for an overview of what's new across the CSD Software Portfolio over the last 12 months: https://www.ccdc.cam.ac.uk/solutions/whats-new/
The University of Michigan has an unlimited site license to access CSD. You may access the database via either of the following two means.
1. WebCSD - the online portal to the CSD (Click here to access WebCSD)
2. Install Cambridge Structural Database System (CSDS) on your own computer.
If you are running on Windows or Linux, you should be able to install the latest updates seamlessly by simply clicking on Help > Check for Updates in either Mercury or Hermes. If you experience any problems, or you are running on Mac OSX, you will need to download and install the updates manually from the CCDC website: https://www.ccdc.cam.ac.uk/support-and-resources/downloads/
You can find out more about the updates from this blog article on the CCDC website: https://www.ccdc.cam.ac.uk/
With version 2020.3 as a minimum which is available from the ITAM share you install normally but instead of running the activator you only need to set an environment variable (at least on Linux) to point to the license server.
You have access to CSD-Crossminer, a tool that allows crystal structure databases such as the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB) to be searched in terms of pharmacophore queries. Intuitive pharmacophore queries describing, among others, protein−ligand interaction patterns, ligand scaffolds, or protein environments can be built and modified interactively. Matching crystal structures are overlaid onto the pharmacophore query and visualised as soon as they are available, enabling the user to quickly modify a hypothesis on the fly. This delivers an overall interactive search experience with application in the areas of interaction searching, scaffold hopping or the identification of novel fragments for specific protein environments.
For example use cases, please see:
Korb O, Kuhn B, Hert J, Taylor N, Cole J, Groom C & Stahl M “Interactive and Versatile Navigation of Structural Databases” J Med Chem, 2016, 59(9):4257, DOI: 10.1021/acs.jmedchem.5b01756.
This release enables:
• Python 3.7 as the default version for all CSD applications
• The CSD Python API will be Python 3 enabled straightaway at the point of installation
• Easy integration with other key scientific Python packages
This release will incorporate Python 3 by default, with the miniconda version of the CSD Python API bundled within the 2020.0 CSD Release running on Python 3.7. This means that the CSD Python API will be Python 3 enabled straight away at the point of installation and easy to integrate with other key scientific Python packages like TensorFlow, scikit-learn, matplotlib, pandas and RDKit.
Find out more here: https://www.ccdc.cam.ac.uk/
For CSD Python API example scripts, download .zip file.