Cambridge Structural Database (CSD) is a world wide repository of small molecule crystal structures hosted by Cambridge Crystallographic Data Center (CCDC). The 2020.0 release contains over 1,034,174 entries (1,016,168 unique structures), an increase of more than 60,000 entries! The new release contains the following new features:
1) The launch of polyhedral display in Mercury
2) Python 3 compatibility
3) Support in the CSD Python API for all types of 3D query available in ConQuest
4) Extension of th CSD-CrossMiner database
5) Seamless, flexible searching of CSD and PDB data
6) Molecular interaction maps in the CSD Python API
6) Polymer expansion in Mercury
University of Michigan has 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.
Two Options to Download
Option 1: Request links to download the software at: http://www.ccdc.cam.ac.uk/supp
Note: The 2020.0 CSD release will require a complete re-installation of the software and data. You will need the Customer No. and Activation Key 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.
The availability of the CSDS for different operating systems is explained in the box below.
The difference between WebCSD and the CSDS client access is explained in the tab WebCSD and CSDS.
The 2020.0 CSD Release installer contains:
For downloading from M+Box Folder
Updating to Mac OS X 10.10 can cause an existing XQuartz installation to become corrupted. For OS X 10.8 and later a suitable X11 server can be downloaded from http://xquartz.macosforge.org.
Find more troubleshooting tips on the CCDC Support page.
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.
To download CSD Crossminer (64-bit only), use Option 1 or Option 2 and refer to installation notes. For Option 2, refer to the table below:
Download .zip file for Windows 7/8 and 10, Windows Vista, or Windows XP .
Download .dmg file for Mac OS X 10.8, 10.9, 10.10, and 10.11.
Download 64-bit installation files for Linux.
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.
To download Python 3.7. CSD Python API 3.0.0, use Option 1 or Option 2 and refer to installation notes. For Option 2, refer to the table below: