Software Licensed by the Science Library: Features and Tools
Components of CSD Enterprise
Provides essential search, visualization and analysis features of known small-molecule organic and metal-organic crystal structure data from the Cambridge Structural Database (CSD). Includes 2D/3D searching, extensive geometry analysis tools, intermolecular interaction analysis, high impact graphics and connectivity via the CSD Python API.
A crystal structure database with advanced 3D searching. More advanced than the WebCSD, including context and criteria matching, to quickly identify structures based on a wide range of properties. Obtain big-data insights with multiple search options by substructure, reference, unit cell, and text terms including known polymorphs and subsets.
Use the CSD System programmatically. Create tailored scripts using the whole spectrum of CSD functionality with this fully customizable API (Application Programming Interface). Automate in-depth searching and chemical analyses of the crystal structure data. The API Technical documentation for this application is available.
See chemistry in 3D and generate high-definition, customized images, animations, and 3D models of molecules. Analyse chemical and physical properties with informatics-based insights drawn from empirical data in the Cambridge Structural Database (CSD). Use Mercury, in combination with other CCDC data and software, to discover new drugs and molecules and develop new materials.
Validate the geometry of experimental or predicted structures and predict the likely chemical conformations before a structure has been determined. Get a rapid, accurate assessment of molecular conformations such as small molecule structure validation, protein–ligand docking pose assessment, structure design, and more.
Visualize proteins, DNA, and other macromolecules. Generate high-definition images or animations. Perform docking, generate conformers, overlay ligands, and more. Apply all these features to published or new structures — Hermes can open many common file formats including .mol2 .mol .pdb .mmCIF and .sdf.
Understand how crystal structures pack in the solid state and the related physical properties. Data from IsoStar can be used in SuperStar for pharmacophore generation and prediction of intermolecular interactions. Provides interactive 3D scatterplots that show the probability of interactions between functional groups.
Generates interaction maps within protein binding sites or around small molecules, i.e. it predicts ‘hot-spots’ where a chosen interaction type is particularly favorable. Interaction maps are generated by estimating the probability of an interaction based on how often the interaction has been observed in crystal structures.
A widely recognized protein–ligand docking software based on a genetic algorithm. It is known for its high accuracy in predicting ligand binding and flexibility in handling diverse drug discovery protein docking scenarios. Identify and optimize potential drug candidates by predicting how small molecules, or ligands, interact with their target proteins.
Pharmacophore-based data mining search of structural databases. Build custom pharmacophore queries and simultaneously mine the CSD, PDB, and your proprietary structural data to quickly identify off-target effects, alternative scaffolds, similar binding sites, interaction motifs, bioisosteres, and more. Filter results based on knowledge of the target and binding site, or block areas those already tested.
In-house database editing software. Store your crystallographic files in a private ‘cloud’ and create in-house databases that can be shared with colleagues or can be downloaded for use in CSD-Core desktop tools such as ConQuest and Mercury. Can be searched independently of or in conjunction with the CSD. Available for Windows and Linux.
Access data from the Protein Data Bank, the Cambridge Structural Database, and in-house database(s). Perform advanced searching across protein-ligand binding sites and small molecule structures, including 2D and 3D search. Understand how the interactions, conformations, and behaviour you observe for a given target-ligand pair compares to existing observed systems.
The Crystallographic Information File (CIF) is the internationally agreed standard file format for information exchange in crystallography. EnCIFer enables users to validate CIFs and ensure their files are format-compliant for deposition with journals and databases or for storage in laboratory archives.
Community Tools
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.
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.
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.
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.
Integrated Partner Software
CSD data and software is integrated with various complementary products from our key software partners to provide even more functionality. Additional third-party software is available for free to CSD subscribers for integration with other components of the CSD Enterprise.
In 2022 Dassault Systèmes’ BIOVIA integrated CCDC’s trusted protein-ligand docking algorithm, GOLD, into their cloud-based 3DEXPERIENCE® platform. This brings together GOLD’s scientific excellence with the flexibility and scalability of the cloud.
CSD KNIME Nodes Component Collection
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.
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.
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
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 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.
