CncTranslate Cheminformatics Utility
CncTranslate is a central component of ChemNavigator's software tool kit for cheminformatics data management and analysis. CncTranslate is used to perform file conversion among many chemical structure file formats and to calculate properties on chemical structure databases. CncTranslate offers a full command line interface and may be used as a cheminformatics utility program within other applications. A restricted version of CncTranslate is available for immediate download from our web site. Please contact us to receive access keys for a full evaluation.

The table below summarizes the current CncTranslate options available today.

CncTranslate Option Overview
CncTranslate Basic Basic includes tools for file conversion between standard chemical structure file formats and graphical display formats common to the cheminformatics industry. Click here to see a table of supported formats.
CncTranslate Advanced The Advanced option includes rules based structure normalization and validation of structure representation. It also includes tools for creation and enumeration of variable structures including macro groups, Markush representations, Tautomers, and adjusting protonation states.
CncTranslate 3D The 3D option allows approximate 3D coordinates to be calculated for 2D structures. Click here to learn more about our 3D coordinate generation tool.
CncTranslate Drug-Like The Drug-Like option permits the calculation of commonly used molecular descriptors including: molecular weight, counts of hydrogen-bond donors & acceptors, the number or rotatable bonds. This tool also permits the definition and counting of custom molecular fragments.
CncTranslate Search The Search option enables searching of chemical structure lists in SLN format. Search enables the searching functionality for data items and substructure chemical searching. Search may be applied to large files and is commonly used as a flat-file based cheminformatics system.
CncTranslate RGroups The RGroups option enables the R-group decomposition functions. These functions locate a core substructure within each chemical structure in an input series, and determine the R-groups that are attached to it for each structure in the input set. The input is a core substructure pattern and a structure file containing the series of chemical structures for analysis. The output includes each input structure with the identified core marked and any R-groups as molecular fragments. A common source for the input core substructure pattern is the ChemNavigator CncMCS program.


CncTranslate Basic Supported File Formats

Format Type
Input
Output
MDL SD Files
Yes
Yes
SMILES
Yes
Yes
Tripos SYBYL Line Notation (SLN)
Yes
Yes
JME Format (Novartis Java Editor)
Yes
Yes
Tripos MOL2
Yes
Yes
PNG Graphics
N/A
Yes
2D Coordinate Generation
N/A
Yes
2D bitmap fingerprint generation
N/A
Yes
Protein Databank Format (PDB)
Yes
Yes


CncTranslate 3D Background
The 3D option for CncTranslate allows the rapid calculation of approximate 3D coordinates for drug-like chemical structures. The coordinates are calculated by forming many rough 3D geometries for each molecule based upon assembling pre-calculated 3D molecular fragments. Each assembled molecule is then conformationally relaxed using our Tweak-Flex algorithm developed by Dr. Tad Hurst. The output of this program is a single reasonable 3D conformation for each drug-like molecule in the data set. The output 3D confirmations do not attempt to reach to fully relaxed 3D geometries but do form very suitable starting geometries for other 3D search techniques such as 3D searching or docking.




CNC Translate Highlights
Download CNC Translate and try it within your company's research program.

For more information, please contact a business development representative at CNC_Support@sial.com.

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