How to use AlphaFold2 for Wet Lab Researchers
Вставка
- Опубліковано 26 лип 2021
- My effort to explain how to use the Alphafold2 algorithm to predict the structure of a protein without having a lot of bioinformatics knowledge.
I am mostly a wet lab researcher and I know that a lot of us are far from confident in our bioinformatics skills. That is why it was important to me to publish this video, so more people can benefit from this amazing technology.
Links:
Blog post on Alphafold2
deepmind.com/blog/article/put...
Alphafold Protein Structure Database on ebi website
alphafold.ebi.ac.uk/
Alphafold GitHub page to download the code
github.com/deepmind/alphafold
alphafold Colab page to run it on the cloud
colab.research.google.com/git...
Colab Pro to have more computational resources
colab.research.google.com/signup
Such an underrated video, thanks for explanation!
Thanks! Great explanation.
thank you so much!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I am waiting for the continuation
Thank you!!
I have two peptides with 17 residues each, one is head to tail cyclic peptide and the other is stapled peptide. Does alphafold2 work with chemically modified peptides?
Hey Reza, could you please make a tutorial for using rosettafold please? Maybe that's possible to run locally since the requirements are lower?
I think there is also a full online version of rosettafold that I can record a video on it and for that I don't think there is any need for a local version. For alphafold the local version uses the full database and the online one uses a smaller database. So, the local's result is more accurate in some cases.
@@rezarezaei4868 hi Reza,
Yes I did some digging yesterday and found that the Baker lab website has an online submission point so it is easy enough to look at individual proteins- however I am unsure of how to build complexes (I heard that if you just add a flexible linker and repeat the monomer N Times that can work, so might try that with the server submission)
at the time of installing the database is shows error "Error: aria2c could not be found. Please install aria2c (sudo apt install aria2)." in spite of having aria2 installed.
Hello Reza what to do in case you want to predict a dimer?
Hi, actually I haven't tested this myself but I read that if you put a monomer first and then a hundred X and then the sequence of the second polypeptide, you can predict the dimer structure. But I'm not sure how accurate that would be. There have been some interesting results using this method! However, the current version does not natively support dimers.
The champion of computer illiterate wet lab researchers xD Cheers mate, great video!
U should have made it clear for those who don't have any dependencies what should they do
"damet garm" from Stockholm xD
What are your computer parameters? The minimum requirements for running it?
I think the minimum is at least 8 gb of gpu and 32gb of ram. Also you need around 3Tb of fast storage for having a local copy of all the libraries.