08. Creating Single sdf Files for Docking, 8.1 Manipulating Text Files

8. Creating Single sdf Files for Docking

8.1 Manipulating Text Files

To run your molecular docking experiments, you will need a single sdf file containing the full list of compounds you wish to dock in that experiment. This sdf file must contain 3D conformation information for your compounds (see section 6). You might already have a suitable sdf from searching an online database (see section 5), in which case you can directly use this sdf for docking experiments. However, you may have designed your own compounds in ChemDraw, which means you may need to perform some text file manipulation to combine these files together.

There are hundreds of different chemistry file formats, some include display information (boxes, highlighted substructures, legends etc), some are designed for capturing out from quantum calculations, others are designed for biomolecules or polymers.

The sdf file format has become a widely adopted standard for exchange of small molecule information, it has the advantage of being plain text, it can accommodate both 2D and 3D structures, and a file can contain multiple records.

In a single ChemDraw document you can fit quite a lot of designs, for the purposes of this tutorial we have just drawn one compound (in each file), however this process is easily applied to a file with multiple compounds in.

When saving your designs (save as…) you can choose to save the file as a sdf rather than a cdx file. This will allow you to open up your designs in DataWarrior and ultimately use them for docking experiments.

Doing this will cause ChemDraw to display a warning box about this not being a native file for ChemDraw, you can just click ok.

You can open your sdf file as a text file by opening it in your text file editor (for us this is Notepad, on a Mac you will use TextEdit), to do this right click on the file, then click open with, then select your text editor.

This will open up the rather scary view of your file in text format:

Depending on how many designs you had in your ChemDraw file, scrolling down will allow you to see all of the compounds that you have saved in this file. The “$$$$” indicates the end of a compound’s entry.

Let’s say you had 2 ChemDraw documents filled with designs of compounds you wish to test in docking experiments. Once you have saved these ChemDraw files as sdf files (as above) you can open each file as a text file and view them in your text editor.

Now you can highlight all of the compounds in one file and copy and paste them into the other files text file.

If you wanted to select only certain compounds from one file you could do this in the exact same way, stopping after the “$$$$” for the final compound.

Copy and pasting the second file into the first file (paste after the $$$$ of the last compound in the first file) will effectively merge the two files together.

Here we merged two files containing just one compound each, but this can be done with any number of compounds.

After merging you should check the molecule title (in this case Compound2.sdf) is unique. This is sometimes a problem if you have molecules from different sources. You can of course use more descriptive titles, such “ChangedEsterToAmide”

Once you have your files merged correctly you can save the new text file as a single sdf for docking (file, save as…).

Just type in .sdf at the end of your file name and hit save.

You can now view this sdf file in DataWarrior to analyse the properties of all of your designed compounds and filter as necessary (see section 6). Once your sdf file is fit for docking and contains 3D structure information you can go ahead and dock your compounds.