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galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry
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Suggested tools for drug discovery #64

Open chrisbarnettster opened 4 years ago

chrisbarnettster commented 4 years ago

Based on discussions from gitter https://gitter.im/usegalaxy-eu/Lobby @praveenkumarpgiindia

Does Galaxy have a tool to predict the synthetic reaction of drugs? Or to evaluate between different synthetic reactions for a compound? Some options : Chemical synthesis is the biggest rate-limiting step in drug discovery and galaxy with its world-class implementation pattern should go ahead in overcoming it. I am hereby providing some of the open-source tool/ literature in this regard - OSET: Organic Synthesis Exploration Tool (https://github.com/cekkr/oset) ; Cantera (https://cantera.org/) ; https://link.springer.com/article/10.1186/s13321-018-0269-8; RDkit in python --> RDkit reaction management; ReactPRED: a tool to predict and analyze biochemical reactions; Computer-Assisted Retrosynthesis Based on Molecular Similarity; Computational prediction of chemical reactions: current status and outlook

These may be more suitable for use in Interactive Jupyter notebooks but worth a look.

simonbray commented 4 years ago

The Cantera library looks interesting. Not sure I have time for such a big project though.

Maybe some simple tools based on the RDKit reaction capabilities would be less time-intensive.

praveenkumarpgiindia commented 4 years ago

OK, Simon. Thats great to hear. After my exams get over in April, I will also participate in the development.

Regards, Praveen Kumar M

On Tue, Mar 10, 2020 at 3:38 PM Simon Bray notifications@github.com wrote:

The Cantera library looks interesting. Not sure I have time for such a big project though.

Maybe some simple tools based on the RDKit reaction capabilities would be less time-intensive.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/issues/64?email_source=notifications&email_token=AEUDCVXSAQIN3YTIPPID6GLRGYGQHA5CNFSM4LEZNKBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEOKY7YQ#issuecomment-597004258, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEUDCVRLYV7RBGMRO3YZ5T3RGYGQHANCNFSM4LEZNKBA .

-- Dr. Praveen Kumar M, D.M., Clinical Pharmacology Resident, Department of Pharmacology, Post Graduate Institute of Medical Education and Research (PGIMER), Chandigarh, Mobile number: +91 8728831787, Email Id: praveenkumarpgiindia@gmail.com My ORCID id is https://orcid.org/0000-0002-9318-1167

simonbray commented 4 years ago

I will also participate in the development.

Great! We would love to have some help. :)