Applications of Chemistry Development Kit

The Chemistry Development Kit (CDK) is computer software and a library written in the Java programming language for cheminformatics and bioinformatics. It is available for Windows, Linux, Unix and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0. The CDK was created at the University of Notre Dame on September 27-29, 2000 by Christoph Steinbeck, Egon Willighagen, and Dan Gezelter (then developers of Jmol and JChemPaint) to provide a common codebase. The CDK is a widely used open-source cheminformatics toolkit that provides data structures representing chemical concepts and methods for manipulating and performing computations on such structures. The library implements a wide variety of cheminformatics algorithms, from chemical structure normalization to molecular descriptor computation and pharmacophore sensing. It is used in drug discovery, metabolomics, and toxicology.

Our Services Based on Chemistry Development Kit

CDK is a Java library for structural chemistry and bioinformatics. CDK can achieve higher accuracy than existing widely used or state-of-the-art methods. On the CDK platform, CD ComputaBio can provide the listed services:

• Our Services in Bioinformatics
  • Protein active site detection
  • Cognate ligand detection
  • Metabolite identification
  • Pathway databases
  • 2D and 3D protein descriptors
• Our Services in Chemoinformatics
  • QSAR descriptor calculations
  • Coordinate generation and rendering.
  • Canonical identifier for fast and precise searches.
  • Substructure and SMARTS schema searches.
  • Molecule and reaction valence bond representation.
  • Read and write file formats: SMILES, SDF, InChI, Mol2, CML, etc.
  • Efficient molecular processing algorithms: ring search, kekulisation, aromaticity.

Our Capabilities

Our scientists can provide clients with 2D diagram editing and generation, 3D geometry generation, substructure search using exact structure and SMARTS-like queries, fingerprint calculation, cognate ligand detection, metabolite identification, etc.

Features of Chemistry Development Kit

• Drawing of 2D Graphics
  A Controler2D is an adapter for available input devices, which translates the input into changes to the underlying model, which are again reflected in the view generated by the Renderer2D.
• File Input and Output
  Each file format is represented by two separate classes implementing one of the interfaces. CDK currently supports XYZ MDLmolfile, pdb, and CML IO classes.
• Aromaticity Detector
  According to the well-known Hu-ckel rule, the software checks whether the ring contains 4n+2π electrons. All of its atoms and bonds were labeled as aromatic rings, and the search continued with remaining rings of equal size or smaller, removing rings that were entirely part of larger aromatic systems that had been detected.
• Isomorphism Detection
  Being able to determine whether two chemical structures are the same or whether one structure is a subgraph of the other is one of the most important features of cheminformatics libraries.
• Structure Generators
  This package contains some simple structure generators for use by the SENECA system for computer-aided structure interpretation.