Drawing of Molecular Structures

The 1D 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.

Retrieve nucleotide/amino acid sequence file in fasta format (remove the heading, > line) or prepare text file of sequence in one-letter characters. Rename the file as seqname.seq. Prepare to import the sequence by checking (^) Show sequence bond, Show leaving groups, Amino acid-/DNA-/RNA-1 letter from Sequence options of Chemistry menu. Invoke File-Import—Sequences. Select Amino acid-/ DNA-/RNA-1 letter. The sequence (with bonds and leaving groups attached) should appear within the draw window. Mark the whole sequence with Select All from the Edit menu or by using Lasso tool. From the Chemistry menu, select Residue — Expand, the 1D (text string) sequence is transformed into the 2D molecular structure. Save it as struname.skc (e.g., heptapeptide, STANLEY as stanley.skc) as shown in Figure 4.12.

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).

To draw 2D molecular structures, the users should refer to ISIS Draw Quick Start (ISIS Draw help) for operating instructions. Draw the basic framework from template tools (horizontal template-tool icons and template pages from Template menu) and drawing tools (vertical drawing-tool icons). The small triangular sign on the drawing tool icons indicates additional tools available for selection. For example, pressing on the Single bond tool provides selection for drawing a double bond or a triple bond. Verify the chemistry of sketch by clicking run Chemisrtry inspector icon (or select Chemistry inspector from the Chemistry menu). To ensure uniform bond lengths and angles for the sketched molecule, select the molecule and then choose Objects-Clean Molecule. Save the sketch as struname.skc.

To place template, click one of the template-tool icons or an atom/bond in the structural fragment/molecule on the template page and place the template anywhere inside the window by clicking an empty area. The template can be fused/attached to an existing bond/atom by simply clicking the bond/atom. To draw bonds, click a bond tool (Single/double/triple bond or Up wedge/down wedge/either/up bond/ down bond), and then click the drawing area or drag the mouse from an existing atom to add a bond. To sprout a bond from an atom, click a bond tool and then click the atom. To draw chain in one direction/ring of specific shape, click chain/multibond tool. To draw atoms, click Atom tool and enter atom symbol or choose one from the drop-down list. Arrow tool provides options for drawing a variety of arrows (e.g., unidirection, equilibrium, double-head, and electron-shift arrows, etc., after pressing arrow tool then choosing one of the arrows) for chemical reactions. Use Lasso select tool to select any structure/structural component for

Figure 4.13. Home page for an access to TOPS cartoons.

Figure 4.13. Home page for an access to TOPS cartoons.

editing or relocating. To delete atom/bond/object one at a time, click Eraser tool and then the atom/bond/object. Text tool appends text description to the structures/ reactions.

To search for TOPS cartoons at http://tops.ebi.ac.uk/tops/, select Browse the Atlas of topology cartoons and Browse HTML page version to open the query form (Figure 4.13). Enter PDB ID on the Protein code query box (Chain query box can be left blank). The search may request a choice of the chain (if more than one chains are available) and returns TOPS atlas information listing the protein of your choice and representative protein in atlas. Click to view the TOPS cartoon(s) of the representative protein. Right click on the diagram to save the TOPS cartoon as cartoon.gif.

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