ISIS Draw

A structure drawn by a molecular editor such as ISIS Draw) can be translated by the data conversion program AutoNom into a lUPAC name, and vice versa, by exchanging structure information through a ROSDAL string [18, 19]. 

Chemists have been used to drawing chemical structures for more than a hundred years. Nowadays, structures are not only drawn on papei but they are also available in electronic form on a computer for publications, for presentations, or for the input and outptit with computer programs. For these applications, well-known software such as ISIS/Draw (MDL [31] or ChemWindow (Bio-Rad Sadtier [32]) arc used (see Section 2,12), The structures generated with these programs arc... 

Figure 2-129. Isis/Draw V 2.4 provides six different bond types and various important features for chemical tasi

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First, a quei y must be drawn using the MOL" ISIS/Draw program. By using this reaction query, a eurrent reaction search " can be performed. This type of reaction retrieval compares the starting material and the product of the reaction query with all the reactions in the CIRX database. Both query structures must match exactly, including the implicit hydrogen atoms not shown in the reaction query. In this case, one hit is found in the CIRX databases. 

Chem3D can read a wide variety of popular chemical structure files, including Gaussian, MacroModel, MDL, MOPAC, PDB, and SYBYL. Two-dimensional structures imported from ChemDraw or ISIS/Draw are automatically converted to three-dimensional structures. The Chem3D native file format contains both the molecular structure and results of computations. Data can be exported in a variety of chemical-structure formats and graphics files. 

ISIS Draw, SAR, Excel Desktop modeling and data management Molecular Design Limited, Inc. 

Reaction control is temperature-based, with the system trying to attain the adjusted maximum temperature as rapidly as possible. When employing polar reaction mixtures with a high level of absorption, the output power can be limited to a maximum of 150 W to avoid overheating of the sample. The instmments of the Emrys series come with a comprehensive software package for the creation of protocols, including an ISIS draw surface for graphical description of the reactions. 

MDL Information Services, Inc. offers free software downloads at http // www.mdli.com/cgi/dynamic/downloadsect.html7uid= key= id = 1. These include AutoNom Standard (automatic nomenclature), which generates IUPAC chemical names directly from graphical structures created in ISIS/Draw or registered in ISIS/ Base. 

ISIS/Draw is a chemically intelligent drawing package that enables the drawing of chemical structures using the same intuitive signs and symbols used for paper sketches. It is offered free for academic and personal home use only. 

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). 

Fig. 9. ISIS/Draw interface used for defining or modify RXN files. The atom-to-atom mapping function in ISIS/Draw is used to define the reaction. In this case the reaction taken out of ISIS/Base (Fig. 8) has been modified to make it more generic.

Fig. 15.5. Integration between PGVL Flub and ISIS/Draw. By clicking on any structural box in PGVL Flub window, ISIS/Draw will appear with any molecular structure inside the PGVL Flub structural box if exists. Once the user is done creating or polishing a structure drawing inside ISIS/Draw, a single click on ISIS/Draw will transfer the new structure drawing back to the PGVL Flub structural box, and the ISIS/Draw window will disappear automatically.

ISIS-Draw, MDL Information Systems, Inc. http //www.mdli.com. 

For users who prefer to draw in new structures, the later versions of Chem Draw will deliver a SMILES notation which can be used via cut and paste commands, and ISIS Draw delivers a MOLfile which can be automatically converted to a SMILES file. ACD / LogP uses a proprietary drawing program, MolDraw, which is easy to learn and use. Entry by name in ACD is accomplished via a Dictionary with about 48,000 entries. Drawn structures can be saved to a file, but in version beta 0.9 of ACD/LogP there is no method of batch entry from either SMILES files or MDL MOLfiles. 

The ID nucleotide/amino acid sequences in character format (without index, e.g., fasta format) can be converted into the 2D chemical structures with ISIS Draw, which can be downloaded from MDL Information System at http //www.mdli.com/ download/isisdraw.html for academic use. Install the package by issuing Run command, C Isis Draw23.exe. Launch IsisDraw to open the Draw window. 

Figure 4.12. Two-dimensional structure sketch with ISIS Draw. The two-dimensional structure of a heptapeptide, SerThrAlaAsnLeuGluTyr (without hydrogens), is sketched on the ISIS display window after importing the sequence file in text format (STANLEY).

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