NCI/CADD Group
CADD Group Chemoinformatics Tools and User Services
General Information
About the CADD Group's Chemoinformatics Tools and User Services: read more. Or, visit our new blog at http://cactus.nci.nih.gov/blog.
Searching Databases and Online Services
To search and display chemical structures here, you will need Java/JavaScript to be enabled on your browser.
Look up whether a structure occurs in any of tens of different databases, both public and commercial. Currently loaded pointers to: over 74 million entries from more than 100 databases, representing more than 46 million unique chemical structures.
A web service to the open NCI database compounds (>250,000 structures) with different kinds of output features and links to other services for continued processing.
This service works as a resolver for different chemical structure identifiers and allows to convert a given structure identifier into another representation or structure identifier. It can be used via a web form or a simple URL API. Beta version.
Converts graphical representations of chemical structures in journal articles, patent documents, textbooks, trade magazines etc., into SMILES. OSRA can read over 90 graphical formats including GIF, JPEG, PNG, TIFF, PDF, PS etc.
Computer-generated GIF and PNG images of chemical structures for WWW pages etc. from your 2D or 3D input files. Forms-based interface, automatic generation of 2D display coordinates for structures without them.
Web-based SMILES Translation Service. Converts SMILES strings, SDF, PDB, MOL and other formats into USMILES, and SDF, PDB and MOL file formats.
Generation of VRML scenes from your 2D or 3D data files. Automatic generation of 3D coordinates if not contained in the input structure. Many display options to control the visual appearance.
Pseudo-Rotational Online Service and Interactive tool (PROSIT). Calculates, and displays in tabular format, the pseudorotation parameters (P, chi, nu_max) and other useful information for 3D structures of nucleosides, nucleotides and analogs thereof, as well as for DNA and RNA single and double strands, whether by themselves or complexed with a protein. You can request a visual output of the found nucleoside (analog) or (oligo-)nucleotide in 2D or 3D.
Pseudorotation Visualization: Ancillary tool to modify the pseudorotation parameters P and nu_max interactively, and observe the resulting conformational changes in a 3D model of a five-membered ring.
Tools, Data, and Links
Toolkit (programmed in Perl 5) providing functions to read and parse structure files in MDL's SDF format, such as filter and add/remove properties, select individual records out of large SD files etc. A Windows version is also available.
A fast clustering program for computation of a representative subset of a large dataset. Applicable, but not limited, to chemical databases.
Here you can download the "raw" data in bulk format that were used in building the Enhanced NCI Database Browser.
A list of URLs that point to other public chemical (or chemistry-related) information. Currently limited to U.S. Government web sites. These sites may contain search capabilities and/or other public datasets.
A table of searchable small molecule databases available on the web, listing URLs and an (incomplete) survey of the services' features and capabilities. Contains (U.S.) Government, academic, and commercial web sites.
M. C. Nicklaus (Content), M. Sitzmann (New scheme)
Last Update: 2009-07-31
The NCI/CADD group is a research unit within the Laboratory of Medicinal Chemistry (LMC).
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