Simplified Molecular Input Line Entry System SMILES

3 SIMPLIFIED MOLECULAR INPUT LINE ENTRY SYSTEM (SMILES) 

SMILES is a line notation developed in the 1980s and since modified and extended by others, particularly Daylight Chemical Information Systems, Inc. 

Using simple rules, a structure is represented by a string of characters unique to that structure. It can also be used to specify stereochemistry at double bonds and chiral centres. SMARTS is a further extension that allows substructure searching. 

SMILES strings may be converted back to two-dimensional structures using structure diagram generation programs, of which there are several on the market. 

See Kelson, H. E., Structure diagram generation, in Reviews in Computational Chemistry, ed. K. B. Lipkowitz and D. B. Boyd (New York Wiley-VCH, 1999), pp. 313-398. 

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Toropov AA, Toropova AP, Mukhamedzhanova D, Gutman I (2005a) Simplified molecular input line entry system (SMILES) as an alternative for constructing quantitative structure-property relationships (QSPR). Indian J. Chem. Sect A. 44 1545-1552. 

The Simplified Molecular Input Line Entry System (SMILES) is frequently used for computer-aided evaluation of molecular structures [1-3]. SMILES is widely accepted and computationally efficient because SMILES uses atomic symbols and a set of intuitive rules. Before presenting examples, the basic rules needed to enter molecular structures as SMILES notation are given. 

As described in Chapter 9 there are an increasing number of commercial toxicological prediction systems available. Naturally these have been designed to be user friendly most run under Microsoft Windows and use the Simplified Molecular Input Line Entry System (SMILES) as the molecular input. It is therefore possible to obtain a prediction of toxicity instantaneously, and often this may be performed for large numbers of compounds. There is a great temptation to use predicted toxicities at face value (i.e., if a compound is predicted to be non-toxic then it must be non-toxic). This simplistic use of predicted values should be avoided at all costs. Ideally, there are a number of criteria that should be applied when predicting toxicity. It is essential that a trained expert uses the predictive system. The user should be an expert both in the endpoint being predicted and the use of the predictive system. 

The most commonly used identifiers today include line notation identifiers (e.g., Simplified Molecular Input Line Entry System [SMILES] and International Chemical Identifier [InChls]), tabular identifiers (e.g., Molfile and Structure Definition [SD] file types), and portable mark-up language identifiers (e.g., Chemical Markup Language [CML] and FlexMol). Each identifier has its strengths and weaknesses as detailed in Chapter 5. Chapters 5 and 6 provide enough information to guide researchers in choosing the most appropriate formats for their individual use. 

Simplified Molecular Input Line Entry System (SMILES) is a simple, yet complete description of molecular structure that considers the atoms and bonds in a molecule. Using unique canonical SMILES, an indexed table lookup of a structure can be quickly done. For example, the SQL to lookup phenol is ... 

The use of Simplified Molecular Input Line Entry System (SMILES) as a string representation of chemical structure makes possible much of what has been discussed in earlier chapters of this book. A chemical reaction could be represented as a collection of SMILES, some identified as reactants and some as products. It is possible to define a table to do this, or perhaps use some arrays of character data types, but a syntax extension of standard SMILES allows reaction to be expressed easily. SMIRKS is an extension of SMILES and SMiles ARbitrary Target Specification (SMARTS). It is used to represent chemical transformations. SMIRKS can also be used in a transformation function to combine SMILES reactants to produce SMILES products. 

Simplified Molecular Input Line Entry System (SMILES)... 

The Simplified Molecular Input Line Entry System (SMILES) is the most popular line notation in use today, and though it technically remains a proprietary product of Daylight Chemical Information Systems Inc., it has been widely implemented by other vendors. Unfortunately this has led to some divergence of dialects of the notation, especially with respect to extensions to... 

JME Molecule Editor is a Java applet to draw/edit structures and reactions [21], It also displays molecules on screen in display panel and generates output formats like Simplified Molecular-Input Line-Entry System (SMILES) and MDL molfile. To use JME in your portlet, use the following applet code. Include the JME distribution containing JME.jar for referencing. 

The Simplified Molecular Input Line Entry System (SMILES) strings ofthe structures in the data set were canonicalized, the charges were standardized, the additional fragments and salts were removed, and duplicate or invalid structures were identified and removed using the KNIME workflow environment [29]. Further data quality control was performed by the Eli Lilly AD ME group. 

The scheme can be based not only on molecular graphs, but also on simplified Molecular Input Line Entry System (SMILES) [24—26]. SMILES contains an string of characters. These characters reflect molecular stmcture, or at least some part of attributes of the molecular stmcture. Based on such assumptions one can attempt to define a descriptor that represents a mathematical function of the SMILES characters. Figure 12.2 contains the scheme for building up optimal descriptors using SMILES. 

The simplified molecular input line entry system (SMILES) [68-71] is a compact and comfortable representation of the molecular structure from a chemical point of view. An increasing munber of SMlLES-based databases are gradually appearing on the internet, and thus it is interesting and important to search for suitable ways of using such a representation in QSPR-QSAR analyses. It has to be noted that the molecular graph contains details of the molecular architecture which is absent in SMILES. For instance, an extended connectivity of increasing order cannot be calculated directly from this notation. 

Although many systematic indices (e.g.. Lipid MAPS, Chemical Entries of Biological Interest (ChEBI), lUPAC International Chemical Identifiers (InChl), simplified molecular-input line entry system (SMILES)) were developed to list the chemical compounds, these indices (identifiers) can only be meaningful if the compound is totally identified. However, in practice, lipidomics analysis in many cases can only provide partial identification of lipid molecular structures at the current development of technology. Moreover, different lipidomics approaches provide different levels of stmctural identification of lipid species. Therefore, how to clearly express and report the information about the levels of identification for the structures of lipid species (which can be derived fi om MS analysis) is not only helpful for the readers but also important for bioinformatics and data communication. To this end, the analysis by shotgun lipidomics could be used as a typical example to explain these levels. Similar phenomena also exist in the analysis of lipid species employing LC-MS-based approaches. 

Fortunately, such molecular description exists under simplified molecular-input line-entry system (SMILES) form initially developed as a computational (ASCII strings) entry it has certain features making it an ideal candidate for present purpose (Weininger, 1988 Weininger et al., 1989 ... 

Here we like to test the performance of the SPECTRAL-Diagonal stmc-ture-activity relationship (SD-SAR) methodology of Section 3.2.2 (Putz, 2013a), against the ordinary QSAR analysis, see Section 2.4.3, for the anti-HTV class of chemical compounds of Section 3. 3.7. 1, either for genuine (as in gas-phase), or Simplified Molecular Input Line Entry System (SMILES) (as in cellular environment, see Section 3. 2.9) molecular forms. 

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