MDL ISIS/Draw

Fig. 2 Reactions at the hydroxyl groups of glycosyl residues of oligo-/polysaccharides. (A) Basic a(l 4) linked glycosyl residue. (B) Oxidation at C6 position to form uronic acid. (C) Oxidation/substitution at C2 position to form acetate. (D) Oxidation/ substitution at C2 position to form glucosyl-2-amine. (E) Oxidation/substitution/compatibilization at C2 position to form glucosyl-2-A-acetyl. (F) Oxidation/substitution/compatibilization at C4 position compatibilization glycosyl-4-sulfate. (G) Oxidation/activation at C6 position compatibilization glucosyl-6-phosphate. (Molecular modeling SWEET, http //www.dkfz-heidelberg.de/spec/sweet2/doc/index.php. Chemistry MDL ISIS/draw.) (View this art in color at www.dekker.com.)...

Fig. 4 Solubility of polysaccharides iu aqueous medium. (A) Hydration/possible H bonds for a sequence of o-Glcp P(l—>4)-D-Glcp (cellobiose). (B) Scheme for cahbration of equilibrium distances due to repulsive electrostatic and attractive van der Waals forces. (Chemistry MDL ISIS/draw. Graphics Macromedia Fireworks.) (View this art in color at www.dekker. com.)...

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... 

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. 

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. 

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). 

This is the standard library design scenario which is supported by most in-house and commercial vendor tools. The user-defined reaction is usually a Markush reaction drawing commonly in the format of MDL ISIS sketch or. rxn file (35). Chemists may also supply reactant sets for each reaction component either by loading pre-defined sets of molecules or by retrieving them via searches into chemical reactant databases. Molecular property calculations and analysis on the reactants are performed, and selections are made based on these results. This is commonly known... 

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. 

The new versions of DfW are compatible with Microsoft Windows. For the prediction of toxicity the chemical structure of a compound is input into the system with the use of ISIS/Draw (from MDL Information Systems) or by importing a mol-file or sd-file (Figure 2a). After the system has the structure, pushing the process button starts the prediction. During processing, the system searches and identifies all known toxicophores in the structure from all the different toxicological endpoints within seconds. After completion of the analysis, the system opens a result window. The result window contains the imported structure, a list of toxicological endpoints that the system has made a prediction for, the number and name of... 

ISIS/Draw Elsevier MDL, 14600 Catalina Street, San Leandro,CA 94577.Commercial http //www.mdli.com/products/framework/isis draw/index.jsp. Freeware http //www.mdli.com/downloads/downloadable/index.jsp. MDL will ultimately discontinue ISIS/Draw and replace it with Mol Draw. 

Starting with a structure entered with MDL ISlS/Draw or imported as MDL Molfile or ISIS Sketch files (.skc), the user can define constraints to restrict the reported metabolites. Unconstrained generation of metabolic pathways from a compound would lead to combinatorial explosion of the amount of metabolites. Constraints can be defined for the following ... 

ISIS/Draw 2.1, MDL Information Systems, 14600 Catalina Street, San Leandro, CA. 

A limited version of ISIS/Draw at the Elsevier MDL website (free registration required)... 

Those who choose to search a private database such as one created with MDL s ISIS must learn a different set of search techniques. ISIS /Draw, the ISIS chemical drawing package, is a presentation package for polymer structures. ISIS/Draw allows scientists to draw polymer structures with ease and speed, and then to search and share them. Researchers also have the enhanced capability of accessing 2D and 3D databases, with a wide range of search options and a link to global data. ISIS/Draw includes full annotation capabilities, which enable researchers to label collections of atoms or bonds with related function or process information (6). 

HyperChem provides several options for structure input. An intuitive drawing tool allows quick sketching of structures, which are easily converted to three-dimensional structures with the Model Builder. Biomolecules (DNA, RNA, and proteins) can be assembled quickly using the biomolecule residue iibraries. Structure editing features are versatile and available at all times. HyperChem also reads files stored in the foiiowing formats Brookhaven PDB, MDL ISIS Sketch, MDL MOL, MOPAC Z-Matrix, Sybyl MOL2, and ChemDraw CHM. 

The software standardizes functional group representation and molecular structures according to common chemical rules (e.g., MDL conventions). It is useable as an add-on for ISIS/DRAW to prevent erroneous structure (reaction) drawing. 

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