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- Lensink, Marc F., et al.
(författare)
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Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment
- 2023
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Ingår i: Proteins. - : WILEY. - 0887-3585 .- 1097-0134.
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Tidskriftsartikel (refereegranskat)abstract
- We present the results for CAPRI Round 54, the 5th joint CASP-CAPRI protein assembly prediction challenge. The Round offered 37 targets, including 14 homodimers, 3 homo-trimers, 13 heterodimers including 3 antibody-antigen complexes, and 7 large assemblies. On average similar to 70 CASP and CAPRI predictor groups, including more than 20 automatics servers, submitted models for each target. A total of 21 941 models submitted by these groups and by 15 CAPRI scorer groups were evaluated using the CAPRI model quality measures and the DockQ score consolidating these measures. The prediction performance was quantified by a weighted score based on the number of models of acceptable quality or higher submitted by each group among their five best models. Results show substantial progress achieved across a significant fraction of the 60+ participating groups. High-quality models were produced for about 40% of the targets compared to 8% two years earlier. This remarkable improvement is due to the wide use of the AlphaFold2 and AlphaFold2-Multimer software and the confidence metrics they provide. Notably, expanded sampling of candidate solutions by manipulating these deep learning inference engines, enriching multiple sequence alignments, or integration of advanced modeling tools, enabled top performing groups to exceed the performance of a standard AlphaFold2-Multimer version used as a yard stick. This notwithstanding, performance remained poor for complexes with antibodies and nanobodies, where evolutionary relationships between the binding partners are lacking, and for complexes featuring conformational flexibility, clearly indicating that the prediction of protein complexes remains a challenging problem.
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| 2. |
- Tendulkar, Shriharsh P., et al.
(författare)
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The 60 pc Environment of FRB 20180916B
- 2021
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Ingår i: Astrophysical Journal Letters. - : American Astronomical Society. - 2041-8213 .- 2041-8205. ; 908:1
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Tidskriftsartikel (refereegranskat)abstract
- Fast radio burst FRB 20180916B in its host galaxy SDSS J015800.28+654253.0 at 149 Mpc is by far the closest-known FRB with a robust host galaxy association. The source also exhibits a 16.35 day period in its bursting. Here we present optical and infrared imaging as well as integral field spectroscopy observations of FRB 20180916B with the WFC3 camera on the Hubble Space Telescope and the MEGARA spectrograph on the 10.4 m Gran Telescopio Canarias. The 60-90 milliarcsecond (mas) resolution of the Hubble imaging, along with the previous 2.3 mas localization of FRB 20180916B, allows us to probe its environment with a 30-60 pc resolution. We constrain any point-like star formation or H ii region at the location of FRB 20180916B to have an H alpha luminosity L-H alpha less than or similar to 10(37) erg s(-1), and we correspondingly constrain the local star formation rate to be less than or similar to 10(-4) M yr(-1). The constraint on H alpha suggests that possible stellar companions to FRB 20180916B should be of a cooler, less massive spectral type than O6V. FRB 20180916B is 250 pc away (in projected distance) from the brightest pixel of the nearest young stellar clump, which is similar to 380 pc in size (FWHM). With the typical projected velocities of pulsars, magnetars, or neutron stars in binaries (60-750 km s(-1)), FRB 20180916B would need 800 kyr to 7 Myr to traverse the observed distance from its presumed birth site. This timescale is inconsistent with the active ages of magnetars (less than or similar to 10 kyr). Rather, the inferred age and observed separation are compatible with the ages of high-mass X-ray binaries and gamma-ray binaries, and their separations from the nearest OB associations.
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