Question: how to find different properties of a list of drugs ?
1
gravatar for Mo
3.5 years ago by
Mo40
/
Mo40 wrote:

Hello,

I have a list of drugs , I would like to know which type of informations can I retrieve for them and using which galaxy ? any information is appreciated. 

 

 

 

drugs galaxy enrichment • 1.0k views
ADD COMMENTlink modified 2.0 years ago by muratiskar0 • written 3.5 years ago by Mo40

This might be a good start for you: https://open.fda.gov/

ADD REPLYlink written 3.5 years ago by Martin Čech ♦♦ 4.8k
3
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening5.1k
Germany
Bjoern Gruening5.1k wrote:

Hi Mo,

you need to use a special Galaxy instance that is focused on cheminformatics. Please have a look at:

https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox

and here is a Docker container with all the tools you will need, including drug-ability predictions, similarity search and various chemical property calculations.

https://registry.hub.docker.com/u/bgruening/galaxy-chemicaltoolbox/

Hope this helps,

Bjoern

ADD COMMENTlink written 3.5 years ago by Bjoern Gruening5.1k

@Bjoern Gruening this for sure helps, but as it is really a galaxy and hard to find information there, is there any example or good tutorial to use ? 

ADD REPLYlink written 3.5 years ago by Mo40

Tutorial for what? Using the chemicaltoolbox or Galaxy?

ADD REPLYlink written 3.5 years ago by Bjoern Gruening5.1k

@Bjoern Gruening for both, I installed the boot2docker but honestly I have no idea how I can use it to search for drug-ability predictions, similarity search or whatever possible. if it is possible, can you give me an example ? 

ADD REPLYlink written 3.5 years ago by Mo40

This is really simple, you have a lot of tools included. Upload your chemicals as SDF, SMILES, InChI's and Galaxy can inter-convert them or you can use different tools on these data sets. For example there is one tool called: "Drug-likeness quantitative estimation (QED)". Try to run it!

ADD REPLYlink written 3.5 years ago by Bjoern Gruening5.1k

@Bjoern Gruening the problem is that there is not any explanation of how to use them! There could be million functions but when they don't write how to invoke them or use them, do you think it is useful? even a simple uploading data is not explained. These are the main problem of mine since I have never used galaxy and I don't where to start 

ADD REPLYlink written 3.5 years ago by Mo40

Ah! You are searching for a general Galaxy Introduction! Here we have excellent material:

https://wiki.galaxyproject.org/Learn

This should help with any Galaxy instance, independent of Genomics, Cheminformatics, Proteomics ...

ADD REPLYlink written 3.5 years ago by Bjoern Gruening5.1k
0
gravatar for muratiskar
2.0 years ago by
muratiskar0
muratiskar0 wrote:

Hi Mo,

You can have a look at "Chemical Annotation Retrieval Toolkit" from http://cart.embl.de/.

It is possible to query drug names to find the PUBCHEM IDs. Then, you can retrieve various chemicals annotations together with the enriched terms.

ADD COMMENTlink written 2.0 years ago by muratiskar0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 107 users visited in the last hour