Simplified Molecular Input Line Entry System

In 1986, David Weininger created the SMILES Simplified Molecular Input Line Entry System) notation at the US Environmental Research Laboratory, USEPA, Duluth, MN, for chemical data processing. The chemical structure information is highly compressed and simplified in this notation. The flexible, easy to learn language describes chemical structures as a line notation [20, 21]. The SMILES language has found widespread distribution as a universal chemical nomenclature... 

SMILES Simplified Molecular Input Line Entry System... 

For each selected PFC, a profile was edited including the name of the compound, its CAS (Chemical Abstracts Service) number and the SMILES (Simplified Molecular Input Line Entry System) formula. 

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. 

SMILES (Simplified Molecular Input Line Entry Systems) is a line notation system based on principles of molecular graph theory for entering and representing molecules and reactions in computer (10-13). It uses a set of simple specification rules to derive a SMILES string for a given molecular structure (or more precisely, a molecular graph). A simplified set of rules is as follows ... 

Computer-Aided Property Estimation Computer-aided structure estimation requires the structure of the chemical compounds to be encoded in a computer-readable language. Computers most efficiently process linear strings of data, and hence linear notation systems were developed for chemical structure representation. Several such systems have been described in the literature. SMILES, the Simplified Molecular Input Line Entry System, by Weininger and collaborators [2-4], has found wide acceptance and is being used in the Toolkit. Here, only a brief summary of SMILES rules is given. A more detailed description, together with a tutorial and examples, is given in Appendix A. 

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. 

In addition to these publications, software is available that allows the user to determine vapor pressures of a wide variety of compounds at room temperature. The Texas Research Center (TRC) (1996) distributes a PC DOS/Windows database that contains experimentally derived Antoine constants for approximately 6000 chemicals from which vapor pressures at user-selected temperatures can be calculated. Another Windows-based program, MPBPVP by Meylan and Howard (1996), estimates the vapor pressure of organic compounds from their SMILES (Simplified Molecular Input Line Entry System) structure and their boiling points using the Antoine equation, the Grain-Watson method, and the Mackay method. 

For abbreviation of analyte names see Sect. Abbreviations , log P logarithm of octanol/water partition coefficient n.c. not calculable as N-atom of tropane moiety is present as alkylated quaternary amine, pKb negative decadal logarithm of base constant, SMILES simplified molecular input line entry system... 

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. 

SMILES simplified molecular input line entry system http //www.daylight.com/smiles/index.html. National Institutes of Health Assay Guidance Manual Version 5.0 http //www.ncgc.nih.gov/guid-ance/manual toc.html. 

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. 

The name SMILES comes from Simplified Molecular Input Line Entry System (Weininger 1988). It is a linear format for description of molecules and reactions developed by Daylight Chemical Information Systems, Inc. SMILES was designed with the intention to be both human readable and writable, which makes it unique among the other chemical formats described in this chapter. 

SIMPLIFIED MOLECULAR INPUT LINE ENTRY SYSTEM (SMILES)... 

WEN and SMILES fragments correspond respectively to substrings of the Wiswesser Line Notation or Simplified Molecular Input Line Entry System strings used for encoding the chemical structures. Since simple... 

SMILES Simplified molecular input line entry system... 

SMILES (Simplified Molecular Input Line Entry System) was invented by Weininger5 to facilitate the representation and manipulation of molecular structures using computers. It uses standard atomic symbols to represent atoms and the symbols - for single bond, = for double bond, and for triple bond. Hydrogen atoms can be represented explicitly but are almost always represented implicitly using normal conventions of valence bond theory. Single bonds need not be explicitly written. For example, propane is C-C-C or simply CCC. Methylamine is CN, and C N is hydrogen cyanide. Propene is C=CC. For more complex structures with branched bonds, parentheses are used. For example, CC(C)0 is isopropyl alcohol, whereas CCCO is propanol. 

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. 

WOMBAT 2006.1 contains 154 236 entries (136 091 unique SMILES Simplified Molecular Input Line Entry System [17, 18]), covering 6801 series from over 6791 papers with more than 307 700 activities for 1320 unique targets. All biological activities are automatically converted to the — log10 of the molar concentration, regardless of activity type. Numerical values for activity are stored in three fields the additional two fields capture the experimental error, when reported1 . Besides exact numeric values (the vast majority), WOMBAT... 

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... 

The UM-BBD-PPS predicts all possible metabolic pathways based on its metabolic rules [10]. The user draws a structure or enters a SMILES (Simplified Molecular Input Line Entry System) string representing the compound of interest. The PPS identifies funcfional groups and matches them to appropriate rules. First-round metabolites are produced. Any first-round metabolite can be selected, and used to match another set of rules. When no metabolic rules are matched, the cycle is stopped. This could indicate a non-metabolizable compound or, in other cases, it is an endpoint metabolite that is a common intermediary compound. 

Alternative to hash coding, USMILES (Unique Simplified Molecular Input Line Entry System) codes may be used that even allow restoring the chemical structures [2],... 

---