How to use Google Colab Alphafold2 and ChimeraX
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- เผยแพร่เมื่อ 19 ส.ค. 2024
- 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 kamryndiehl57@gmail.com
The most informative video on TH-cam that accually worked. Thank you a lots!
dude, how are you so cool. how did tell so many important things in under 5 minutes!!!!!?!?!?!?!?
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.
Thanks so much! I'm on it :)
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.
Most concise and informative video on alphafold2!
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!
Many thanks! Very helpful!♥
Hey there, please continue making more vids like this, Thx!
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!
Great Video!
Very helpful, thank you a lots!
Thanks
super cool!
Good video
Can we prepare multimer of a protein with alphafold?
There is new update on alphfold 3 could you please make an tutorial on that
Can you please explain how to get a written results after matching both pdf files
Very helpful! What is the difference between the individual models that alphafold provides and how do you choose which one to take?
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.
Why is it that I feel like this needs to be done through some UI and thereby make it so much easier? 😅
what if I am not getting PDB file in the output folder? what could be a problem?
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 (kamryndiehl57@gmail.com) if the problem is persisting?
I have the same problem
Were you able to solve the problem?
@@LauraMuller-pn9nh yes. Just save the file with extension. Pdb, and you will be able to use it