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.
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
@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 ?
Tutorial for what? Using the chemicaltoolbox or Galaxy?
@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 ?
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!
@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
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 ...
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.
This might be a good start for you: https://open.fda.gov/