AlphaFold2 examples from CASP 14
From Proteopedia
(Difference between revisions)
| Line 13: | Line 13: | ||
The quality of predictions for the structure of ORF8 are judged by comparison with X-ray crystallographic [[empirical models]] which were not available to the groups making predictions. Shortly after the CASP 14 competition (summer 2020), two X-ray crystal structures were reported for ORF8: [[7jtl]] released August 26, 2020, and [[7jx6]], released September 23, 2020. The [[resolution|resolutions]] are 2.0 and 1.6 Å respectively, and both have worse than average [[Rfree]] values. | The quality of predictions for the structure of ORF8 are judged by comparison with X-ray crystallographic [[empirical models]] which were not available to the groups making predictions. Shortly after the CASP 14 competition (summer 2020), two X-ray crystal structures were reported for ORF8: [[7jtl]] released August 26, 2020, and [[7jx6]], released September 23, 2020. The [[resolution|resolutions]] are 2.0 and 1.6 Å respectively, and both have worse than average [[Rfree]] values. | ||
{{Template:Green links zoom}} | {{Template:Green links zoom}} | ||
| - | <scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene>: 87 of the 102 residues/chain align with a [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions root mean square deviation] '''(RMSD) of 0.66 Å'''<ref>Alignment and RMSD calculation was by ''iterative magic fit'' of Swiss PDB Viewer.</ref>. | + | <scene name='87/875686/Morf_lin_7jx6_imf_7jtl/3'>The two X-ray structures agree very well</scene>: 87 of the 102 residues/chain (85%) align with a [https://en.wikipedia.org/wiki/Root-mean-square_deviation_of_atomic_positions root mean square deviation] '''(RMSD) of 0.66 Å'''<ref name="imf">Alignment and RMSD calculation was by ''iterative magic fit'' of Swiss PDB Viewer.</ref>. When sidechains are included, 829 atoms (90% of 918 total) aligned with RMSD 4.3 Å<ref name="mf">Alignment and RMSD calculation was by ''magic fit'' of Swiss PDB Fiewer.</ref>, and 348 atoms (38%) aligned with RMSD 0.71 Å<ref name="imf" />. |
===AlphaFold2 Prediction for ORF8=== | ===AlphaFold2 Prediction for ORF8=== | ||
| - | The quality of a prediction in CASP is judged, in large part, by the [[Theoretical_models#CASP_14_Global_Distance_Test_Results|Global Distance Test Total Score, GDT_TS]]. AlphaFold2's predicted structure<ref>Download AlphaFold2's predicted structure for ORF8 from [https://predictioncenter.org/casp14/MODELS_PDB/T1064-D1/T1064TS427_1-D1.pdb T1064TS427_1-D1.pdb].</ref> has a '''GDT_TS score of 87'''. (A score of 0 is meaningless, and a score of 100 means perfect agreement with an X-ray crystal structure.) 87 means the model is close to the accuracy of an X-ray crystal structure. The structure predicted by AlphaFold2 is almost as close to the X-ray crystallographic model [[7jx6]] as is the independently-determined X-ray structure [[7jtl]]. AlphaFold2 predicted the positions of 92 amino acids. CASP 14 excluded residues 48-59, a 12-residue surface loop, from the target residues<ref name="casp14domains" />. | + | The quality of a prediction in CASP is judged, in large part, by the [[Theoretical_models#CASP_14_Global_Distance_Test_Results|Global Distance Test Total Score, GDT_TS]]. AlphaFold2's predicted structure<ref>Download AlphaFold2's predicted structure for ORF8 from [https://predictioncenter.org/casp14/MODELS_PDB/T1064-D1/T1064TS427_1-D1.pdb T1064TS427_1-D1.pdb].</ref> has a '''GDT_TS score of 87'''. (A score of 0 is meaningless, and a score of 100 means perfect agreement with an X-ray crystal structure.) 87 means the model is close to the accuracy of an X-ray crystal structure. The structure predicted by AlphaFold2 is almost as close to the X-ray crystallographic model [[7jx6]] as is the independently-determined X-ray structure [[7jtl]]. AlphaFold2 predicted the positions of 92 amino acids. (CASP 14 excluded residues 48-59, a 12-residue surface loop, from the target residues<ref name="casp14domains" />.) 83 amino acids alpha carbons in the prediction aligned with those in [[7jx6]] with an RMSD of 1.25 Å<ref name="imf" />. When sidechains are included, |
Revision as of 20:09, 23 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, verified by the bi-annual prediction competition CASP, please see 2020: CASP 14. Below are illustrated some examples of predictions from that competition.
| |||||||||||
References
- ↑ 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
- ↑ 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.
- ↑ 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
- ↑ 4.0 4.1 Summary and Classifications of Domains for CASP 14.
- ↑ 5.0 5.1 5.2 Alignment and RMSD calculation was by iterative magic fit of Swiss PDB Viewer.
- ↑ Alignment and RMSD calculation was by magic fit of Swiss PDB Fiewer.
- ↑ Download AlphaFold2's predicted structure for ORF8 from T1064TS427_1-D1.pdb.
