CASP Results: AlphaFold has solved the structure prediction Grand Challenge

Started by Susume

beta_helix Staff Lv 1

Yep, Seth sent this around to the Foldit team this morning.

We're going to discuss it at our Foldit meeting later today… it merits a news post, don't you think? ;-)

beta_helix Staff Lv 1

and they had an entire slide about Foldit!

Will post more after the conference ends later today, but wanted to pass this on :-)

Susume Lv 1

I love this passage from Janet Thornton, Director Emeritus of the European Bioinformatics Institute:

"As a lover of everything protein, the most exciting thing for me is that this breakthrough is not an end, but a whole new beginning, bringing with it electrifying opportunities and follow-on questions. The structures allow us to understand better how the proteins function and, in turn, this could enable us to fine-tune this function for the benefit of people and the planet. Just like the Human Genome Project facilitated the birth of new scientific disciplines, such as genomics, solving the protein structure question could bring about new and exciting fields of research. One thing is for sure, it’s a fine time to be a protein scientist!"

https://www.ebi.ac.uk/about/news/opinion/AlphaFold-protein-structure-prediction

Susume Lv 1

CASP/AlphaFold have released the slides from their talk at the CASP conference - kinda hard to follow without the talking part, but interesting nonetheless:

Also here is a long and thoughtful piece about what this advance means for the field:

Bruno Kestemont Lv 1

(In French) very good video explaining how Deep Learning works.

Note:
-the importance of a large amount of data
-the usefulness of an intermediary algorithm where Human describes the relevant characteristics to look for
-the detrimental effect of false classifications in the database

Neural networks with deep learning are not able to propose names for plants and animals on a photo, like in this Belgian-Netherlands Citizen Science project here:
https://eur.observation.org
(you post a picture of an European species, the system proposes you a species name. When it's >80% probability, you further check then ask for a validation by experts => the database enrich all the time with validated observations - it now only works well for BE-NL species).

Susume Lv 1

A tweet today from Demis Hassabis, CEO of DeepMind:
@demishassabis
Brief update on some exciting progress on #AlphaFold! We’ve been heads down working flat out on our full methods paper (currently under review) with accompanying open source code and on providing broad free access to AlphaFold for the scientific community. More very soon!

Also, a very interesting graphic showing where AlphaFold2, trRosetta, Rosetta, and a menagerie of other protein modeling methods fall on the continuum between big-data-based and biological-knowledge-based approaches can be found in a recent review in Cell Systems at:
https://www.cell.com/cell-systems/fulltext/S2405-4712(21)00203-9</>