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More on SMILES

SMILES is an acronym for Simplified Molecular Input Line Entry System. It is a simplified chemical notation that allows a user to represent a 2 dimensional chemical structure in linear textual form for easy entry into a computer application. SMILES supports representation of some 3D characteristics, such as bold and hatched bonds and cis/trans, as well as charged and complexed molecular entities. The SMILES code in standard usage today uniquely generates a single molecular structure, but the reverse is not true, i.e. a molecular structure can be represented by multiple SMILES code strings.

SMILES notation is commonly employed in the QSAR (Quantitative Structure-Activity Relationship) community in modeling applications, and is used as well in some commercial and public software for prediction of chemical properties and biological activities. For general information on SMILES, links are provided below to a number of on-line SMILES tutorial guides as well as some on-line application sites that use SMILES chemical data entry.

On-line SMILES Tutorials
On-line SMILES Translator
Examples of Websites and Applications Using SMILES Structure Input

For more information on SMILES generation and usage in DSSTox SDF files, see:
More on DSSTox Standard Chemical Fields

On-line SMILES tutorials:

DayLight Chemical Information Systems, Inc. SMILES Tutorial
The most comprehensive information on SMILES, offering both a lengthy on-line manual as well as shorter tutorial. Also provides links to variety of modeling applications that use SMILES, and an on-line SMILES-to-structure converter.
http://www.daylight.com/smiles/f_smiles.html exit EPA

Syracuse Research Corporation's SMILECAS Notations Description
Provides a lengthy tutorial and description of SMILE notation, with examples.
http://www.syrres.com/esc/docsmile.htm exit EPA

U.S. Environmental Protection Agency, Mid-Continent Ecology Division-Duluth, (MED-Duluth) SMILES Tutorial
Provides a relatively short and simple tutorial with basic rules for SMILES construction.
http://www.epa.gov/med/Prods_Pubs/smiles.htm

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On-line SMILES Translator:

NCI Structure Browser CACTVS Tools
Free web-based SMILES Translation Service (04/02) with expanded input and output formats. Converts SMILES strings, SDF, PDB, MOL and other formats into USMILES (Unique SMILES exit EPA), and SDF, PDB and MOL file formats. The service automatically recognizes SDF files (single and multiple structure), text files with multiple SMILES fields, MOL files and PDB files (and in fact any other format CACTVS recognizes). User can submit SMILES strings or create a SMILES string using the Structure Editor.
http://cactus.nci.nih.gov/services/translate/ exit EPA

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Examples of Websites and Applications Using SMILES Structure Input:

Persistent, Bioaccumulative, and Toxic Profiles Estimated for Organic Chemicals On-Line
http://www.pbtprofiler.net/ exit EPA
http://www.pbtprofiler.net/information.asp exit EPA

pbt profiler graphic exit EPA

SPARC On-Line Property Calculator
Using a SMILES input, calculates physical-chemical properties such as pKa, hydrolysis, etc; also has a SMILES to structure display feature.
http://ibmlc2.chem.uga.edu/sparc/index.cfm exit EPA

TORVS Research Team
Incudes on-line access to CACTVS Chemical Information System and CORINA 3D structure calculator, with SMILES input.
http://www2.ccc.uni-erlangen.de/software/index.html exit EPA

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