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Mehmet Akdel, Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros, Patrick Bryant, Lydia L. Good, Roman Aleksander Laskowski, Gabriele Pozzati and 24 more
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
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Akdel, M., Pires, D. E. V., Porta‐Pardo, E., Jänes, J., Zalevsky, A. O., Mészáros, B., Bryant, P., Good, L. L., Laskowski, R. A., Pozzati, G., Shenoy, A., Zhu, W., Kundrotas, P. J., Ruiz‐Serra, V., Rodrigues, C. H. M., Dunham, A. S., Burke, D. F., Borkakoti, N., Velankar, S. S., … Beltrão, P. (2022). A structural biology community assessment of AlphaFold2 applications. Nature Structural & Molecular Biology, 29(11), 1056–1067. https://doi.org/10.1038/s41594-022-00849-w
Akdel, Mehmet, et al. "A structural biology community assessment of AlphaFold2 applications." Nature Structural & Molecular Biology, vol. 29, no. 11, 2022, pp. 1056–1067, https://doi.org/10.1038/s41594-022-00849-w.
Akdel, Mehmet, Douglas E. V. Pires, Eduard Porta‐Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros, Patrick Bryant, et al. "A structural biology community assessment of AlphaFold2 applications." Nature Structural & Molecular Biology 29, no. 11 (2022): 1056–1067. https://doi.org/10.1038/s41594-022-00849-w.
Akdel M., Pires D. E. V., Porta‐Pardo E. [и др.] A structural biology community assessment of AlphaFold2 applications // Nature Structural & Molecular Biology. — 2022. — Vol. 29, № 11. — P. 1056–1067. — URL: https://doi.org/10.1038/s41594-022-00849-w
@article{akdel2022structural,
title = {{A structural biology community assessment of AlphaFold2 applications}},
author = {Mehmet Akdel and Douglas E. V. Pires and Eduard Porta‐Pardo and Jürgen Jänes and Arthur O. Zalevsky and Bálint Mészáros and Patrick Bryant and Lydia L. Good and Roman Aleksander Laskowski and Gabriele Pozzati and Aditi Shenoy and Wensi Zhu and Petras J. Kundrotas and Victoria Ruiz‐Serra and Carlos H. M. Rodrigues and Alistair S. Dunham and David F. Burke and Neera Borkakoti and Sameer S Velankar and Adam S. Frost and J. Basquin and Kresten Lindorff‐Larsen and Alex G. Bateman and Andrey V. Kajava and Alfonso Valencia and Sergey Ovchinnikov and Janani Durairaj and David Benjamin Ascher and Janet M. Thornton and Norman E. Davey and Amelie Stein and Arne Elofsson and Tristan Ian Croll and Pedro Beltrão},
journal = {Nature Structural \& Molecular Biology},
year = {2022},
volume = {29},
number = {11},
pages = {1056--1067},
doi = {10.1038/s41594-022-00849-w},
url = {https://doi.org/10.1038/s41594-022-00849-w}
}TY - JOUR AU - Akdel, Mehmet AU - Pires, Douglas E. V. AU - Porta‐Pardo, Eduard AU - Jänes, Jürgen AU - Zalevsky, Arthur O. AU - Mészáros, Bálint AU - Bryant, Patrick AU - Good, Lydia L. AU - Laskowski, Roman Aleksander AU - Pozzati, Gabriele AU - Shenoy, Aditi AU - Zhu, Wensi AU - Kundrotas, Petras J. AU - Ruiz‐Serra, Victoria AU - Rodrigues, Carlos H. M. AU - Dunham, Alistair S. AU - Burke, David F. AU - Borkakoti, Neera AU - Velankar, Sameer S AU - Frost, Adam S. AU - Basquin, J. AU - Lindorff‐Larsen, Kresten AU - Bateman, Alex G. AU - Kajava, Andrey V. AU - Valencia, Alfonso AU - Ovchinnikov, Sergey AU - Durairaj, Janani AU - Ascher, David Benjamin AU - Thornton, Janet M. AU - Davey, Norman E. AU - Stein, Amelie AU - Elofsson, Arne AU - Croll, Tristan Ian AU - Beltrão, Pedro TI - A structural biology community assessment of AlphaFold2 applications JO - Nature Structural & Molecular Biology VL - 29 IS - 11 SP - 1056 EP - 1067 PY - 2022 DA - 2022/11/01 DO - 10.1038/s41594-022-00849-w UR - https://doi.org/10.1038/s41594-022-00849-w ER -
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