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alphafold pipeline  (SIB Swiss Institute of Bioinformatics)
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SIB Swiss Institute of Bioinformatics alphafold pipeline
Classification performance of AlphaFold2 models predicted for the physiological and non-physiological homo dimers of the benchmark dataset. This is evaluated on the subset of 1480 targets for which results were produced with all AlphaFold2 versions. Column 1 lists the version of <t> AlphaFold </t> used for the predictions, and the score used to quantify the similarity between the AlphaFold2 predicted model, and the homodimer structures of the corresponding benchmark entry (see Main text for detail). Column 2 lists the Area Under the Curve (AUC) of the ROCs computed using the listed scores. Columns 3 and 4 list the mean and median values for the computed scores considering only the physiological dimers. Those for the non-physiological dimers are not reported, as AlphaFold2 tends to predict alternative association modes for a significant fraction of these dimers, as expected.
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Classification performance of AlphaFold2 models predicted for the physiological and non-physiological homo dimers of the benchmark dataset. This is evaluated on the subset of 1480 targets for which results were produced with all AlphaFold2 versions. Column 1 lists the version of AlphaFold used for the predictions, and the score used to quantify the similarity between the AlphaFold2 predicted model, and the homodimer structures of the corresponding benchmark entry (see Main text for detail). Column 2 lists the Area Under the Curve (AUC) of the ROCs computed using the listed scores. Columns 3 and 4 list the mean and median values for the computed scores considering only the physiological dimers. Those for the non-physiological dimers are not reported, as AlphaFold2 tends to predict alternative association modes for a significant fraction of these dimers, as expected.

Journal: Proteomics

Article Title: Discriminating physiological from non-physiological interfaces in structures of protein complexes: a community-wide study

doi: 10.1002/pmic.202200323

Figure Lengend Snippet: Classification performance of AlphaFold2 models predicted for the physiological and non-physiological homo dimers of the benchmark dataset. This is evaluated on the subset of 1480 targets for which results were produced with all AlphaFold2 versions. Column 1 lists the version of AlphaFold used for the predictions, and the score used to quantify the similarity between the AlphaFold2 predicted model, and the homodimer structures of the corresponding benchmark entry (see Main text for detail). Column 2 lists the Area Under the Curve (AUC) of the ROCs computed using the listed scores. Columns 3 and 4 list the mean and median values for the computed scores considering only the physiological dimers. Those for the non-physiological dimers are not reported, as AlphaFold2 tends to predict alternative association modes for a significant fraction of these dimers, as expected.

Article Snippet: G.T., L.P., and T.S. acknowledge the contributions of Gabriel Studer in setting up the AlphaFold pipeline for our analysis, sciCORE at the University of Basel for providing computational resources and system administration support, and funding from the SIB Swiss Institute of Bioinformatics and the Biozentrum PhD Fellowships.

Techniques: Produced