AlphaFold2 examples from CASP 14

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Line 39: Line 39:
===Second Best Prediction for ORF8===
===Second Best Prediction for ORF8===
-
In CASP 14, 70 research groups and 42 automated servers predicted structures for ORF8. The median GDT_TS score for all 112 predictions was 26. AlphaFold2 made the best prediction (GDT_TS 87). <scene name='87/875686/Second_best_orf8_imf/1'>The second best prediction was by the group of Xian Ming Pan</scene>, with GDT_TS 43 (see TABLE above). The fold and topology were predicted correctly, but the '''details are far less accurate''' than those in AlphaFold2's prediction. The 2nd best prediction does accurately include the '''three disulfide bonds''' found in the [[empirical models]].
+
In CASP 14, 70 research groups and 42 automated servers predicted structures for ORF8. The median GDT_TS score for all 112 predictions was 26. AlphaFold2 made the best prediction (GDT_TS 87). <scene name='87/875686/Second_best_orf8_imf/1'>The second best prediction was by the group of Xian Ming Pan</scene>, with GDT_TS 43 (see TABLE above). The fold and topology were predicted correctly, but the '''details are far less accurate''' than those in AlphaFold2's prediction. The 2nd best prediction does accurately include the '''three disulfide bonds''' found in the [[empirical models]] (not shown).
===Third Best Prediction for ORF8===
===Third Best Prediction for ORF8===

Revision as of 20:31, 24 February 2021

This page is under construction. Eric Martz 01:03, 22 February 2021 (UTC)

Prediction of protein structures from amino acid sequences, theoretical modeling, has been extremely challenging. In 2020, breakthrough success was achieved by AlphaFold2[1], a project of DeepMind. For an overview of this breakthrough, documented by the bi-annual prediction competition CASP, please see 2020: CASP 14. Below are illustrated some examples of predictions from that competition.

Drag the structure with the mouse to rotate

References

  1. ↑ Senior AW, Evans R, Jumper J, Kirkpatrick J, Sifre L, Green T, Qin C, Zidek A, Nelson AWR, Bridgland A, Penedones H, Petersen S, Simonyan K, Crossan S, Kohli P, Jones DT, Silver D, Kavukcuoglu K, Hassabis D. Improved protein structure prediction using potentials from deep learning. Nature. 2020 Jan;577(7792):706-710. doi: 10.1038/s41586-019-1923-7. Epub 2020 Jan, 15. PMID:31942072 doi:http://dx.doi.org/10.1038/s41586-019-1923-7
  2. ↑ CASP14: what Google DeepMind’s AlphaFold 2 really achieved, and what it means for protein folding, biology and bioinformatics, a blog post by Carlos Outeir al Rubiera, December 3, 2020.
  3. ↑ Flower TG, Buffalo CZ, Hooy RM, Allaire M, Ren X, Hurley JH. Structure of SARS-CoV-2 ORF8, a rapidly evolving immune evasion protein. Proc Natl Acad Sci U S A. 2021 Jan 12;118(2). pii: 2021785118. doi:, 10.1073/pnas.2021785118. PMID:33361333 doi:http://dx.doi.org/10.1073/pnas.2021785118
  4. ↑ 4.0 4.1 Summary and Classifications of Domains for CASP 14.
  5. ↑ 5.0 5.1 Alignment by Swiss-PdbViewer's iterative magic fit. This starts with a sequence alignment-guided structural alignment, and then selects subsets of the structures to minimize the RMSD. Eight intermediate structures were generated by the Theis Morph Server by linear interpolation.
  6. ↑ Download AlphaFold2's predicted structure for ORF8 from T1064TS427_1-D1.pdb.

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz

Retrieved from "http://proteopedia.org/wiki/index.php/AlphaFold2_examples_from_CASP_14"
Personal tools