Simplified molecular input line entry

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... 

A somewhat dilferent way to define a molecule is as a simplified molecular input line entry specification (SMILES) structure. It is a way of writing a single text string that defines the atoms and connectivity. It does not define the exact bond lengths, and so forth. Valid SMILES structures for ethane are CC, C2, and H3C-CH3. SMILES is used because it is a very convenient way to describe molecular geometry when large databases of compounds must be maintained. There is also a very minimal version for organic molecules called SSMILES. 

SMILES (simplified molecular-input line-entry specification) a way of specifying a molecular formula and connectivity, but not the three-dimensional geometry... 

SMILES (for Simplified Molecular Input Line Entry Specification) notations, as a compact molecular representation [8]. 

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. 

RMSEte Root mean square error for the test set RMSEtr Root mean square error for the training set SMILES Simplified molecular input line entry specification... 

SMILES (simplified molecular input line entry... 

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... 

Rule scripts operate on substances defined in a data file in either SMILES (simplified molecular input line entry specification) or CMP (compound) format. The conventional SMILES notation as developed by Weininger [28] provides a basic description of molecules in terms of two-dimensional chemical graphs. The CMP file format developed with the OASIS system [29] provides separate logical records for information about connectivity, three-dimensional structure, electronic structure from quantum-chemical molecular-orbital computations, as well as physicochemical and experimental toxicological data. 

Structure registration is the process of entering structural information in a centralized repository, usually a structure database. These repositories serve as a pool for providing structure information that has been created in other departments of a company. Structure databases are set up according to the individual needs of a department or company. They consist of a common representation of a structure in a standardized file format, such as MolFile, SDF, reaction (RXN) (MDL), JCAMP (International Union of Pure and Applied Chemistry), or simplified molecular input line entry specification. Any additional data can be stored with the structure depending on the context typical examples are structure properties, reaction conditions, and literature references. 

---