Foldy: An open-source web application for interactive protein structure analysis
Fig 2
A. Structure Panel: the left panel in the Structure View displays the structure. This is the predicted structure of a homodimer of the polyketide synthase pik2, with NADPH docked into the AT domain with AutoDock Vina. This structure was rendered with NGLViewer [15]. B. Sequence View: the amino acid sequence is displayed in the Inputs tab, and is optionally annotated with domain predictions, such as the pfam annotations displayed here. C. Predicted Alignment Error: The predicted alignment error, measured in Ångstroms, is an AlphaFold metric. In Foldy it is rendered in the PAE tab with Plotly [16]. This displayed heatmap shows the predicted alignment error for the pik2 homodimer. The relatively low PAE between the KS-AT portions of the two peptides indicates that the two KS-ATs rigidly dimerize, while the comparably high PAE between the KRs and the rest of the structure indicate that the KRs move freely and independently. D. Contact Probability: The contact probability is derived from the internal AlphaFold distance probability distribution function, and can be interpreted as the likelihood that two residues are within 8Å of each other. For residues between disparate chains, this might suggest a contact point between two interacting domains or peptides. The 8Å contact probability is rendered in Foldy on the Contacts tab with Plotly [16]. Displayed is the contact probability for the predicted structure of the pik2 homodimer. Yellow dots in off-diagonal blocks suggest predicted interacting or contacting residues between the two peptides.