How to use Google Colab Alphafold2 and ChimeraX

This is a quick instructional video for the botany lab, but I will make it public in case it can be helpful to anyone else. I tried to keep this video short, so I kept explanations vague. However, I will make more in-depth videos soon if this proves to be useful!
Links:
Colab AlphaFold2 - colab.research...
ChimeraX download - www.rbvi.ucsf....
Uniprot - www.uniprot.org
Feel free to email me with any questions at [e-mail]

[@KaiXu-lu3ub]

The most informative video on TH-cam that accually worked. Thank you a lots!

[@056vatsalapandey3]

dude, how are you so cool. how did tell so many important things in under 5 minutes!!!!!?!?!?!?!?

[@shakiryusop]

Thanks! Brilliant overview for alphafold and Chimera under 5 mins. Would enjoy a more in-depth video, especially on what is next after the matchmaker command e.g., How do one make a conclusion or analysis on the comparison between the wildtype and mutant, etc.

[@kamdiehl]

Thanks so much! I'm on it :)

[@geoffmcfadden7109]

Brilliant, thanks. Using your excellent tutorial, I was able to have a structure predicted from a dinoflagellate gene on Colab AF2 and then match it to a known structure from rice in ChimeraX very quickly not having used either package before. These two genes last shared a common ancestor ~2b years ago, and the aligned structures showed me where the major differences are.

[@ningsui6078]

Most concise and informative video on alphafold2!

[@rezarezaei4868]

Hi, this was a very nice video. I also had a video on using alphafold2 when it was the early days of using it before they predict the structure of every single protein and put it in the ebi database!

[@lezhang91]

Many thanks! Very helpful!♥

[@DigitalStickers]

Hey there, please continue making more vids like this, Thx!

[@JackieMartindale]

Loved this, thanks so much! Pretty sure I just predicted the structure of my mutated T/P53 protein vs. wild type (one of my cancer's simpler missense mutations, l111q) and though I've no idea what to do with it yet, it was a fun exercise. 🙂 Please make more, you're inspiring me to a second career!

[@dgoodall6468]

Great Video!

[@ngocbkhn89]

Very helpful, thank you a lots!

[@albertobertani4822]

Thanks

[@ziixx4633]

super cool!

[@jesperedelfeldtjacobsen4446]

Good video

[@bnratha]

Can we prepare multimer of a protein with alphafold?

[@parthkulkarni2167]

There is new update on alphfold 3 could you please make an tutorial on that

[@mariam-rehan]

Can you please explain how to get a written results after matching both pdf files

[@TheUmbrella1976]

Very helpful! What is the difference between the individual models that alphafold provides and how do you choose which one to take?

[@zhenwang323]

Thank you for your tutorial. I wonder what if it appears the same bug (download fails) when I try to do it through web browser like google chrome. Can I download manually on the left side bar? Which file should I download on the left side bar of the colab web window? By the way, the bug (download fails) only happens for me when I choose all the three options before running predict.

[@Unknown_19870]

Why is it that I feel like this needs to be done through some UI and thereby make it so much easier? 😅

[@razanabbara887]

what if I am not getting PDB file in the output folder? what could be a problem?

[@kamdiehl]

Sorry for the late reply - I've never heard of this problem but would like to help. Could you email me a screenshot of the output folder ([e-mail]) if the problem is persisting?

[@LauraMuller-pn9nh]

I have the same problem

[@LauraMuller-pn9nh]

Were you able to solve the problem?

[@razanabbara887]

@@LauraMuller-pn9nh yes. Just save the file with extension. Pdb, and you will be able to use it