Software Licensed by the Science Library: Support and Resources
The Robin Li and Melissa Ma Science Library has purchased campus-wide site licenses for several products. Access to all of these products is limited to current Stanford students, faculty, and staff.
Support
Contact the CCDC's support team by sending email to support@ccdc.cam.ac.uk
- Learn how to harness cheminformatics and data insights from the CSD.
- Tutorials and guides for hands-on workshops.
- Software training, short how-to video tutorials, new functionality introductions, presentations, instructions, talks and more.
- By integrating crystal structures into your course you will provide your students with the opportunity to visualise and manipulate real molecules in 3D and to work with experimentally-measured data.
- Information derived from the CSD is vital to structural chemistry research in its broadest sense, and in particular to pharmaceutical drug discovery, materials design, drug development and formulation. More than 2,000 papers and reviews [e.g. 2-4] have been published worldwide that describe research applications using the accumulated data in the CSD.
Additional Resources
CSD-Community is a collection of free products and services for the benefit of the scientific community. It covers a wide range of crystallographic tools — from data collection, validation and visualization to teaching, research and analysis.
- DASH
This link opens in a new window
A user-friendly graphical-user-interface-driven computer program for solving crystal structures from X-ray powder diffraction data, optimized for molecular structures. DASH is now open source and available in GitHub here. - CSD Symmetry
- This link opens in a new window
Provides an extremely flexible source of symmetry-related information- including molecular point group, space group, Z, Z’, and the symmetry of the occupied Wyckoff position for molecules in the CSD. Auxiliary tables provide further information such as the symmetry operators of each of the 230 space groups and the symmetry elements of each of the 38 point groups. Built using Microsoft Access (2007) and available as a free download. - CellCheckCSD
- This link opens in a new window
Automated tool for checking unit cells against the CSD during data collection. CellCheckCSD can be downloaded free of charge once a simple registration step has been completed.
Partner software integrates various complementary products from other software partners to provide even more functionality using CSD data. Available for free to CSD subscribers for integration with other components of the CSD Enterprise.
- BIOVIA
- This link opens in a new window
In 2022 Dassault Systèmes’ BIOVIA integrated CCDC’s trusted protein-ligand docking algorithm, GOLD, into their cloud-based 3DEXPERIENCE® platform. - CSD KNIME Nodes Component Collection
- This link opens in a new window
KNIME is the leading data analytics, reporting and integration platform that is free to use and open source! It has a modular data pipelining approach that allows an easy drag-and-drop creation of visual workflows for data manipulation, machine learning and general computation, without the need for complex programming or scripting by the end user. The CSD KNIME Component Collection brings together the powerful workflow and integrations capabilities of KNIME with the accurate data and powerful software within the CCDC Portfolio. - CSD Linker Database
- This link opens in a new window
Scaffold hopping is the replacement of part of a drug molecule with another, whilst retaining the features of the molecule most important for protein binding in their proper geometrical arrangement to interact with the receptor. This technique, particularly when carried out computationally on a protein-ligand crystal structure, is very popular with drug designers. It is used to develop molecules with more desirable physical properties, which escape existing patent coverage, or which may be easier to synthesize. - CSD Pipeline Pilot Component Collection
- This link opens in a new window
Build custom tools for analyzing CSD structural data without writing any code. Put simply, users can access CSD Python API (Application Programming Interface) functionality without the need to write Python scripts. - CSD ReCore Index
- This link opens in a new window
An index for ReCore searches in BioSolveIT’s drug discovery platform SeeSAR. This database of fragments is used for rescaffolding, employing approximately 50 million chemically diverse fragments and observed combinations from the CSD. ReCore is a third-party software from BioSolveIT which facilitates core replacement, fragment merging, scaffold hopping, and fragment growing. - Malvern Panalytical's HighScore Software for Powder Diffraction
- This link opens in a new window
The HighScore software offers X-ray diffraction data treatments, phase identifications, reporting and profile fits. The (semi-) automatic handling of many datasets by configurable batches and similarity analysis are distinguishing features. The combination of HighScore with the CSD database extends phase identifications, structure fits and applications to pharmaceutical, organic and metal-organic structures. - Spark CSD Fragment Database
- This link opens in a new window
Spark is a bioisostere replacement tool. It uses the electrostatic and steric properties of molecules to rank new scaffolds and R-groups. Using Cresset’s field technology, based on the XED force field, Spark is a highly efficient and rich source of new directions for a project. While most Spark databases use calculated conformations for the shapes of the fragments, the Spark CSD fragment database uses the experimentally-determined and expert-curated fragments and conformations from the CSD as a source of novelty giving you confidence in the conformation of the new fragment.
