| 1. |
- 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. |
- Li, Shaowen, et al.
(författare)
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A Multiscale, Dynamic Elucidation of Li Solubility in the Alloy and Metallic Plating Process
- 2023
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Ingår i: Advanced Materials. - 0935-9648 .- 1521-4095. ; 35:47
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Tidskriftsartikel (refereegranskat)abstract
- Li-containing alloys and metallic deposits offer substantial Li+ storage capacities as alternative anodes to commercial graphite. However, the thermodynamically in sequence, yet kinetically competitive mechanism between Li solubility in the solid solution and intermediate alloy-induced Li deposition remains debated, particularly across the multiple scales. The elucidation of the mechanism is rather challenging due to the dynamic alloy evolution upon the non-equilibrium, transient lithiation processes under coupled physical fields. Here, influential factors governing Li solubility in the Li-Zn alloy are comprehensively investigated as a demonstrative model, spanning from the bulk electrolyte solution to the ion diffusion within the electrode. Through real-time phase tracking and spatial distribution analysis of intermediate alloy/Li metallic species at varied temperatures, current densities and particle sizes, the driving force of Li solubility and metallic plating along the Li migration pathway are probed in-depth. This study investigates the correlation between kinetics (pronounced concentration polarization, miscibility gap in lattice grains) and rate-limiting interfacial charge transfer thermodynamics in dedicating the Li diffusion into the solid solution. Additionally, the lithiophilic alloy sites with the balanced diffusion barrier and Li adsorption energy are explored to favor the homogeneous metal plating, which provides new insights for the rational innovation of high-capacity alloy/metallic anodes.
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| 3. |
- Li, Shaowen, et al.
(författare)
-
A Multiscale, Dynamic Elucidation of Li Solubility in the Alloy and Metallic Plating Process
- 2023
-
Ingår i: Advanced Materials. - : Wiley-VCH Verlagsgesellschaft. - 0935-9648 .- 1521-4095. ; 35:47
-
Tidskriftsartikel (refereegranskat)abstract
- Li-containing alloys and metallic deposits offer substantial Li+ storage capacities as alternative anodes to commercial graphite. However, the thermodynamically in sequence, yet kinetically competitive mechanism between Li solubility in the solid solution and intermediate alloy-induced Li deposition remains debated, particularly across the multiple scales. The elucidation of the mechanism is rather challenging due to the dynamic alloy evolution upon the non-equilibrium, transient lithiation processes under coupled physical fields. Here, influential factors governing Li solubility in the Li-Zn alloy are comprehensively investigated as a demonstrative model, spanning from the bulk electrolyte solution to the ion diffusion within the electrode. Through real-time phase tracking and spatial distribution analysis of intermediate alloy/Li metallic species at varied temperatures, current densities and particle sizes, the driving force of Li solubility and metallic plating along the Li migration pathway are probed in-depth. This study investigates the correlation between kinetics (pronounced concentration polarization, miscibility gap in lattice grains) and rate-limiting interfacial charge transfer thermodynamics in dedicating the Li diffusion into the solid solution. Additionally, the lithiophilic alloy sites with the balanced diffusion barrier and Li adsorption energy are explored to favor the homogeneous metal plating, which provides new insights for the rational innovation of high-capacity alloy/metallic anodes.
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