PAE viewer: a webserver for the interactive visualization of the predicted aligned error for multimer structure predictions and crosslinks

The development of AlphaFold for protein structure prediction has opened a new era in structural biology. This is even more the case for AlphaFold-Multimer for the prediction of protein complexes. The interpretation of these predictions has become more important than ever, but it is difficult for the non-specialist. While an evaluation of the prediction quality is pro-vided for monomeric protein predictions by the AlphaFold Protein Structure Database, such a tool is missing for predicted complex structures. Here, we present the PAE Viewer webserver(http://www. subtiwiki.uni-goettingen.de/v4/paeViewerDemo), an online tool for the integrated visualization of predicted protein complexes using a 3D structure dis-play combined with an interactive representation of the Predicted Aligned Error (PAE). This metric allows an estimation of the quality of the prediction. Impor-tantly, our webserver also allows the integration of experimental cross-linking data which helps to inter-pret the reliability of the structure predictions. With the PAE Viewer, the user obtains a unique online tool which for the first time allows the intuitive evaluation of the PAE for protein complex structure predictions with integrated crosslinks.

Automated summary

The development of AlphaFold and its variant AlphaFold-Multimer has revolutionized protein structure prediction in the field of structural biology. However, interpreting these predictions can be challenging for non-experts. To address this issue, the PAE Viewer webserver has been introduced, which provides an integrated visualization of predicted protein complexes and allows the evaluation of prediction quality using the Predicted Aligned Error (PAE) metric. Moreover, it enables the integration of experimental cross-linking data to enhance the interpretation of structure predictions.