I am interested in comparing the molecular structure of a known small molecule compound, say Naphthalene, against a small library of similar compounds. I would like to perform a substructure search of my molecule against the library and then programatically display the results in a way that highlight the differences between the query compound and the library compounds by, for example, coloring all of the differences red.
Has anyone already done this, or have suggestions on the best way to go about this? I see that rCDK can be used for substructure search but I am wondering how to keep track of the differences for downstream display.
thanks, zach cp
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Zach Powers
Hi Zach,
I assume the compounds you will be comparing, will start as either sequence files (FASTA) or the PDB's. I did made a web server, which was generating the pdb for an unknown input sequence by homology modeling. The input sequence was send to BLAST for finding the similar sequences, and highly similar resulting protein's pdb was downloaded from the database and was then sent to MODELLER for building the in-silico structure in 3d. This structure then can be visualized using any molecular visualization software like pymol or swissPdb. On the similar terms, I think you can make a perl script to import molecules in pymol, color the differences after super-imposing the molecules and then export it as an image. Once this is done, you can access it on client side using Perl-CGI or any other web-scripting language. Check this page for a collection of Pymol scripts.
Also, have you looked at SuperPose, its an automated web-server which does the super-imposition of two molecules, for all or some chains. You can also specify thresholds etc. That would be a good point ot start as well, read the paper here.
HTH
Sukhi
Thank You Sukhi. I was not clear enough in my original post, however, as I am interested in looking at small molecule compounds and essentially performing a substructure search.
Gotcha, try having a look at this ppt and this Cytoscape Plugin Idea. I think they would be useful to you or wait for someone's idea to do it with rCDK.
Cheers
This can be done using several visualization tools like
pymol, rasmol , discovery studio visualizer
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