Molfile

To become familiar with structure exchange formats such as Molfile and SDfile... 

Parallel to that the MDL Molfile format (see the Tutorial in Section 2.4.6) developed at Molecular Design Limited (now MDL Information Systems, Inc.) became a de facto standard file format [50]. 

Besides the MDL Molfile formal, other file formats are often used in chemistry SMILES has already been mentioned in Section 2.3.3. Another one, the PDB file format, is primarily used for storing 3D structure information on biological macromolecules such as proteins and polynucleotides (Tutorial, Section 2.9.7) [52, 53). GIF (Crystallographic Information File) [54, 55] is also a 3D structure information file format with more than three incompatible file versions and is used in crystallography. GIF should not be confused with the Chiron Interchange Formal, which is also extended with. cif. In spectroscopy, JCAMP is apphed as a spectroscopic exchange file format [56]. Here, two modifications can be... 

During the process of conversion, a program may drop some information produced by other software because the format conventions cannot handle this additional information. For example, when the J ACMP format is converted to a Molfile, its content is reduced to structural data only, without spectra data. In other cases, a... 

MDL Molfile. mol Molfile the most widely used connection table format ummmdli.com 50... 

SDfile. sdf Structure-Data file extension of the MDL Molfile containing one or more compounds umm.mdli.com 50... 

In order to understand the Molfile format let us look at a sample file and recognize its fundamental structure. For simplicity, some less important details will be omitted in the discussion. For a complete description, users are referred to MDL s CTfile format specification [50],... 

Figures 2-24 and 2-25 present the structure of the ethanal molecule and a corresponding Molfile, respectively. The file was extracted from the Enhanced...

Each Molfile consists of two parts the so-called header block specific to Molfiles (lines 1-3) and a eonnection table - Ctab (lines 4-18), which is fundamental to all MDL s CTfile formats. 

Lines 4—18 form the connection table (Ctah), containing the description of the collection of atoms constituting the given compound, which can be wholly or partially connected by bonds. Such a collection can represent molecules, molecular fragments, substructures, substituent groups, and so on. In case of a Molfile, the Ctah block describes a single molecule. 

Figure 2-27. Counts line of the Molfile s header block from the sample f...

Once the atoms arc defined, the bonds between them arc specified in a bond block. Each line of this block specifies which two atoms are bonded, the multiplicity of the bond (the bond type entry) and the stereo configuration of the bond (there arc also three additional fields that arc unused in Molfiles and usually set to 0). The indices of the atoms reflect the order of their appearance in the atom block. In the example analyzed, V relates to the first carbon atom (see also Figure 2-24). "2" to the second one, 3" to oxygen atom, etc. Then the two first lines of the bond block of the analyzed file (Figure 2-29) describe the single bond between the two carbon atoms C1-C2 and the double bond C2=0-5, respectively. 

The basic idea of specifying the priority of the atoms around a stereocenter in order to obtain a stereodescriptor is also incorporated into the most widespread structure representations, the Molfile and SMILES (see Sections 2.3.3, and 2.4.6). 

A molecule editor can draw a chemical structure and save it, for example as a Molfile. Although it is possible to include stereochemical properties in the drawing as wedges and hashed bonds, or even to assign a stereocenter/stereogroup with its identifiers R/S or E/Z), the connection table of the Molfile only represents the constitution (topology) of the molecule. 

A larger number of features are provided by the ACDStructure Drawing Applet (ACDLabs). Both structures and reactions can be drawn, imported, and also exported. This applet supports Molfiles and has a large, integrated collection of pre-defined templates, which are extensible by the user. Additionally, gif files can be exported. It is not possible to draw or to Lmport/export chemical reactions. 

A SMILES code [22], MDL Molfile [50], or JME s own compact format (one-line representation of a molecule or reaction including the 2D coordinates) of created molecules may be generated. The created SMILES is independent of the way the molecule was drawn (unique SMILES see Section 2.3.3). Extensions to JME developed in cooperation with H. Rzepa and P. Murray-Rust also allow output of molecules in the CML format [60]. 

The applet may also be used in a depiction mode as a molecule viewer (without editing buttons), to visualize molecules. Internal J ME format or M DL Molfiles may be viewed in this way. 

Molfile, SDfile, and PDB-file are the most popular data exchange formats. 

After selection of descriptors/NN training, the best networks were applied to the prediction of 259 chemical shifts from 31 molecules (prediction set), which were not used for training. The mean absolute error obtained for the whole prediction set was 0.25 ppm, and for 90% of the cases the mean absolute error was 0.19 ppm. Some stereochemical effects could be correctly predicted. In terms of speed, the neural network method is very fast - the whole process to predict the NMR shifts of 30 protons in a molecule with 56 atoms, starting from an MDL Molfile, took less than 2 s on a common workstation. 

To demonstrate the use of binary substructure descriptors and Tanimoto indices for cluster analysis of chemical structures we consider the 20 standard amino acids (Figure 6.3) and characterize each molecular structure by eight binary variables describing presence/absence of eight substructures (Figure 6.4). Note that in most practical applications—for instance, evaluation of results from searches in structure databases—more diverse molecular structures have to be handled and usually several hundred different substructures are considered. Table 6.1 contains the binary substructure descriptors (variables) with value 0 if the substructure is absent and 1 if the substructure is present in the amino acid these numbers form the A-matrix. Binary substructure descriptors have been calculated by the software SubMat (Scsibrany and Varmuza 2004), which requires as input the molecular structures in one file and the substructures in another file, all structures are in Molfile format (Gasteiger and Engel 2003) output is an ASCII file with the binary descriptors. 

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/home/home.do is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 4.5 include the facihty to visualize imported data however, two free software programs operate well in this regard. One is MDL Chime described previously in this section. Chime, a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator, supports a wide variety of molecule coordinate formats, including PDB (protein data bank), Molfile (from ISIS/Draw), MOP (MOPAC input hies), and GAU (Gaussian Input hies). 

Chemical representation can be rule-based or descriptive. Here we will give a short description of two popular file formats for molecular structures, MOLfiles (9) and SMILES (10-13), to illustrate how molecules are represented in computer. SMILES is a rule-based format while MOLfile is a more descriptive one. 

A MOLfile usually contains a header block and a connection table (see Fig. 2.1). The header block consists of three lines... 

Fig. 2.1. Illustrative example of a MOLFile for acetaminophen (also known as paracetamol), (a) Molecular structure of acetaminophen, commonly known as Tylenol. Tylenol is a widely used medicine for reducing fever and pain, (b) MOLFile for acetaminophen.

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/. 

One of the most widely used chemical structure-encoding schemas in the pharmaceutical industry is the MDL Connection Table (CT) File Format. Both Molfile and SD File are based on MDL CT File Format to represent chemical structures. A Molfile represents a single chemical structure. An SD File contains one to many records, each of which has a chemical structure and other data that are associated with the structure. MDL Connection Table File Format also supports RG File to describe a single Rgroup query, rxnfile, which contains structural information of a single reaction, RD File, which has one to many records, each of which has a reaction and data associated with the reaction, and lastly, MDL s newly developed XML representation of the above—XD File. The CT File Format definition can be downloaded from the MDL website http //www.mdl.com/downloads/public/ctfile/ctfile.jsp. 

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