| 2. |
- 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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| 3. |
- Usman, Sam A., et al.
(författare)
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Multiple populations and a CH star found in the 300S globular cluster stellar stream
- 2024
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Ingår i: Monthly notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 529:3, s. 2413-2427
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Tidskriftsartikel (refereegranskat)abstract
- Milky Way globular clusters (GCs) display chemical enrichment in a phenomenon called multiple stellar populations (MSPs). While the enrichment mechanism is not fully understood, there is a correlation between a cluster’s mass and the fraction of enriched stars found therein. However, present-day GC masses are often smaller than their masses at the time of formation due to dynamical mass-loss. In this work, we explore the relationship between mass and MSPs using the stellar stream 300S. We present the chemical abundances of eight red giant branch member stars in 300S with high-resolution spectroscopy from Magellan/MIKE. We identify one enriched star characteristic of MSPs and no detectable metallicity dispersion, confirming that the progenitor of 300S was a GC. The fraction of enriched stars (12.5 per cent) observed in our 300S stars is less than the 50 per cent of stars found enriched in Milky Way GCs of comparable present-day mass (∼104.5 M⊙). We calculate the mass of 300S’s progenitor and compare it to the initial masses of intact GCs, finding that 300S aligns well with the trend between the system mass at formation and enrichment. 300S’s progenitor may straddle the critical mass threshold for the formation of MSPs and can therefore serve as a benchmark for the stellar enrichment process. Additionally, we identify a CH star, with high abundances of s-process elements, probably accreted from a binary companion. The rarity of such binaries in intact GCs may imply stellar streams permit the survival of binaries that would otherwise be disrupted.
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