Protein models for "Towards a structurally resolved human protein interaction network"
Protein interaction data and annotations
Human protein pairs known to physically interact were obtained from the Hu.MAP dataset, retaining pairwise interactions with >=0.5 confidence, and most interactions from the HuRI dataset.
Protein complex prediction
To predict protein complexes of pairwise interactions, we used the FoldDock pipeline (Bryant et al., 2021) based on AlphaFold2 (Jumper et al., 2021). We use the option of fused+paired multiple sequence alignments (MSAs) and run the model configuration m1-10-1 as this provides the highest success rate accompanied by a 20-fold speed-up. Both the fused and paired MSAs are constructed from running HHblits on every single chain against Uniclust30. The fused MSA is generated by simply concatenating the output of each of the single-chain HHblits runs for two interacting chains. The paired MSA is constructed by combining the top hit for each matching OX identifier between two interacting chains, using the output from the single-chain HHblits runs.
Towards a complete map of the transmembrane proteome in Yeast and E.Coli
Swedish Research CouncilFind out more...