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Keyword: protein complex structure prediction ×Clear all

3 claims from 2 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

   Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes

   Zhu, Shenoy, Kundrotas and Elofsson · Bioinformatics · 2023

   The authors tested AlphaFold-Multimer on larger protein complexes, compared ways of scoring them, proposed a new interface quality score, pDockQ2, and modelled complexes from the CORUM database.

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   1. UncheckedModelling CORUM protein complexes with AlphaFold-Multimer gave two highly confident structures with no sequence homology to any existing structures.“Finally, we modelled protein complexes (from CORUM) and identified two highly confident structures that do not have sequence homology to any existing structures.”