SMILES string

The flic presented contains 11 data items. The header lines arc property names as used by CACTVS [64, 65], and arc sufficiently self-descriptive. For example, E NHDONORS is the number of hydrogen bond donor.s, E SM1LES" is the SMILES string representing the structure of sulfamidc, and E LOGP is the logP value (octanol/water partition coefficient) for this substance. 

When the button "submit smiles is pressed, the SMILES string is sent to the web server of Molsoft, converted to 3D, and the 3D structure is displayed in a java molecule viewer on an automatically created web page (see Figure 2-139). Unfortunately, the Molsoft server does not support downloading of the 3D structures in a standard file format. 

The TcIcSpcc system offens two ways of reading in a query structure. The structure can be input cither directly as a SMILES string (cf. Section 2,3.3) or via a molecule editor which converts the graphical input into the SMILES string. Figure 10.2-10 gives the input form of TeleSpec. 

Figure 10.2-10. Input form of IR Simulator the structures can be entered either as SMILES strings or via a molecule editor.

The structure of a compound including its stereochemistry can be specified with the graphical molecule editor J M E which converts it into a stereochemically unique SMILES string as search item. Figure 10.3-24a shows how I-glutamatc can be input as query,... 

Compound nomenclature, compound codes, fUPAC names, SMILES strings... 

Start ProPred from ICAS and draw the molecule (or import the mol-file of the molecular structure or specify the SMILES string)... 

NCI. http //dtp.nci.nih.gov/docs/ 3d database/structural Jnformation / smiles strings.html, 2004. 

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 ... 

Illustrative SMILES molecular structures and the corresponding SMILES strings are paired vertically. The numbered arrows on the three cyclic molecular structures are not part of the molecules. They are used to indicate the break points for deriving the corresponding SMILES strings (see text)... 

Note that a single molecule may correspond to many different, but equivalent, SMILES strings. For example, for a given asymmetric molecule, starting from a different asymmetric atom will lead to a different, but equally valid, SMILES string. These various SMILES are called isomeric SMILES. They can be converted to a unique form called canonical SMILES (11). 

SMILES strings are very concise and hence are suitable for storing and transporting a large number of molecular structures, while MOLfiles and its extension SDFiles have the option to store more complicated molecular data such as 3D molecular conformational information and biological data associated with the molecules. There are many other file formats not discussed here. Interested readers can find a list of file types at the following web site http //www.ch.ic.ac.uk/chemime/. 

SMILES string configuration for scaffold and building blocks... 

Use the library editor to create a library file for the compounds under study (Fig. 18.2). Library files are essentially plain text files that contain a record on each line, with an entry identifier and a SMILES string for the... 

Click on the Convert SMILES button to perform the conversion of the linear SMILES strings into 3D coordinates (SDF format). To browse automatically, click the Start Visualizer button for the systematic viewing of the 3D molecular structures from the chemical library (Fig. 18.3). 

It defines two simple methods. The molfileToSmiles() method converts a Molfile string to a Smiles string. The smilesToMolfile() method does the opposite—converting a Smiles string to a Molfile string. They both throw MolstructureConversionException to flag conversion failures. The failure can be caused by exceptions from the vendor implementation or from the CRS code. 

Example 2c) Assuming no experimental values of Kow or S are available, estimate Koc for chlorpyrifos (SMILES String Cl-c(nc(clCl)OP(=S)(OCC)OCC)c(Cl)cl) from MCIs using the following expression (Meylan et al., 1992) ... 

To calculate the value of for trichloroethylene (SMILES String C1C(C1)=CC1), you must first draw out its hydrogen suppressed structure and assign delta values to each of its atoms, as shown below. For 1%, the delta value for each atom is equal to the number of atoms it is bonded to. 

Write SMILES strings for fumaric acid, D-gluconic acid, cholesterol, histidine, and AMP. 

Figure 5.4. Alphabetical list of biochemical compounds at Klotho. The 1D (Smile strings), 2D, and 3D structures of metabolites can be viewed/retrieved from Klotho server.

There are four simple rules to apply for the generation of a SMILES string for most organic compounds ... 

The presence of a branch in the structure raises the question of where to start coding. With the SMILES system it does not matter where one starts. A SMILES interpreter will produce the same structure from any valid SMILES coding for a compound. In some circumstances, such as the system s use in databases, it is necessary to have a unique SMILES string for a molecule. Using a set of rules it is possible to uniquify a SMILES string. 

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