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Status: Unchecked ×Keyword: protein-protein interaction ×Clear all

5 claims from 3 papers

1. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   Improved prediction of protein-protein interactions using AlphaFold2

   Bryant, Pozzati and Elofsson · Nature Communications · 2022

   The authors applied AlphaFold2 to predict heterodimeric protein complexes, and built a score from the predicted interfaces to judge model quality and to tell interacting from non-interacting protein pairs.

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   1. UncheckedAlphaFold2 with optimised sequence alignments produced acceptable-quality models (DockQ ≥ 0.23) for 63% of the heterodimeric protein complexes tested.“We find that the AlphaFold2 protocol together with optimised multiple sequence alignments, generate models with acceptable quality (DockQ ≥ 0.23) for 63% of the dimers.”
   2. Unchecked“From the predicted interfaces we create a simple function to predict the DockQ score which distinguishes acceptable from incorrect models as well as interacting from non-interacting proteins with state-of-art accuracy.”

2. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   AF2Complex predicts direct physical interactions in multimeric proteins with deep learning

   Gao, An, Parks and Skolnick · Nature Communications · 2022

   The authors adapt AlphaFold2 into AF2Complex to predict multi-protein complex structures and direct protein-protein interactions, testing it on benchmark sets, the E. coli proteome and a cytochrome c biogenesis system.

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   1. UncheckedThe neural network models AlphaFold2 built for single proteins can be adapted, without retraining, to predict structures of multi-protein complexes.“Here, we demonstrate that the same neural network models from AF2 developed for single protein sequences can be adapted to predict the structures of multimeric protein complexes without retraining.”
   2. Unchecked“It achieves higher accuracy than some complex protein-protein docking strategies and provides a significant improvement over AF-Multimer, a development of AlphaFold for multimeric proteins.”

3. Biochemistry, Genetics and Molecular Biology › Protein Structure and Dynamics

   AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions

   Omidi, Møller, Malhis, Bui and Gsponer · Proceedings of the National Academy of Sciences · 2024

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   1. Unchecked“Finally, our benchmarking revealed that predictions of IDR interactions can also be successful when using full-length proteins, but not as accurate as with cognate IDRs.”