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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. |
- Wang, Yuqi, et al.
(författare)
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Electrolyte-Mediated Misconception of Carbon-Based Electrode Performance and Beyond in Metal-Ion Batteries
- 2023
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Ingår i: Advanced Energy Materials. - : Wiley-VCH Verlagsgesellschaft. - 1614-6832 .- 1614-6840. ; 13:29
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Tidskriftsartikel (refereegranskat)abstract
- A half-cell that is composed of electrode and metal (e.g., lithium) is the most classical model for examining electrode performance in battery community, by which the voltage versus capacity profile is the important indicator. However, it is found that these results are not all reliable, as a misconception of electrode performance can be caused once the electrolyte is chemically unstable. As a paradigm, it is demonstrated that the diethyl carbonate (DEC) solvent can chemically react with lithium metal to form insoluble and soluble by-products, which can accumulate on the lithium anode to influence the lithium potential and/or migrate to the counter electrode to proceed with the uncompleted electrochemical reactions. The resultant voltage-capacity profile cannot reflect the actual electrode performance, such as the lithium storing capability within the graphite. The reason for this phenomenon is elucidated based on solvation chemistry, particularly the mechanism of mitigating it by introducing ethylene carbonatesolvent to form new hydrogen bonds. The viewpoint is further verified by employing the full cell and also extended in sodium and potassium batteries. This study shows the necessity of discerning the reliability of electrode performance and also sheds light on the importance of designing a compatible electrolyte to examine electrode performance.
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