Example input file for ChemViz2

[rammoha...@gmail.com]

Hi

I have a list of drugs for which I want to see the structural similarity.
I am new to chemoinformatics and it will be nice if the experts in the field can help me figure out answers to the following issues:

How to get the smiles data for my drug list?
I was wondering if there are any example files for working with chemviz2. That will be of great help

Thanks,
Ram

[Scooter Morris]

Hi Ram,

    There are a number of sources for SMILES strings, most notably ChEMBL and PubChem.  Once you have your SMILES strings, to import everything into Cytoscape, just create an excel file with your identifier (if any), the drug name, and the SMILES strings as the columns.  It works best if the column containing the SMILES strings is called: "SMILES".  Then import that into Cytoscape as a "network", but select your identifier as the Source and the name and SMILES strings as source targets.  Don't select anything as Target or interactions.  You'll get a warning that you won't create any edges, but that's ok.  Now you should be able to use chemViz2 to calculate the similarities and display a network with the edges weighted by similarity.

-- scooter

[Rammohan Shukla]

Thanks a lot, Scooter, it is working now.

one more question, I have a list of small molecule say, for instance,  AZD-5438,  PHA-793887,  LDN-193189..... and 100 more.

Is there a fast way to retrieve all the information (including SMILES and receptor type) related to all the drugs in my list in an excel sheet or any tabular format? or do I have to pull them one by one?

thanks,

Ram

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[Scooter Morris]

Hi Ram,

   Unfortunately, no, there is no easy way that I know of without some scripting.  It would certainly be a nice addition to ChemViz2, though, and pretty easy to implement.

-- scooter

On Thursday, August 2, 2018 at 12:12:24 PM UTC-7, Rammohan Shukla wrote:

Thanks a lot, Scooter, it is working now.

one more question, I have a list of small molecule say, for instance,  AZD-5438,  PHA-793887,  LDN-193189..... and 100 more.

Is there a fast way to retrieve all the information (including SMILES and receptor type) related to all the drugs in my list in an excel sheet or any tabular format? or do I have to pull them one by one?

thanks,

Ram

On Thu, Aug 2, 2018 at 11:17 AM Scooter Morris <ssbsm...@gmail.com> wrote:

Hi Ram,

    There are a number of sources for SMILES strings, most notably ChEMBL and PubChem.  Once you have your SMILES strings, to import everything into Cytoscape, just create an excel file with your identifier (if any), the drug name, and the SMILES strings as the columns.  It works best if the column containing the SMILES strings is called: "SMILES".  Then import that into Cytoscape as a "network", but select your identifier as the Source and the name and SMILES strings as source targets.  Don't select anything as Target or interactions.  You'll get a warning that you won't create any edges, but that's ok.  Now you should be able to use chemViz2 to calculate the similarities and display a network with the edges weighted by similarity.

-- scooter

On Tuesday, July 31, 2018 at 4:23:59 PM UTC-7, rammoha...@gmail.com wrote:

Hi

I have a list of drugs for which I want to see the structural similarity.
I am new to chemoinformatics and it will be nice if the experts in the field can help me figure out answers to the following issues:

How to get the smiles data for my drug list?
I was wondering if there are any example files for working with chemviz2. That will be of great help

Thanks,
Ram

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Rammohan Shukla, PhD