ModFOLD9: A Web Server for Independent Estimates of 3D Protein Model Quality

[Display omitted] •ModFOLD9 is a popular tool for independently estimating both the global and local quality of 3D protein models.•The new version integrates 6 additional deep learning-based scoring methods, which have been retrained on high-quality model data.•These improvements have led to significant performance increases over the previous versions of the server.•The server results pages provide user-friendly visualisations of annotated models and a refinement option to fix detected errors at the click of a button.•The server has maintained its position as one of the leading methods according to independent benchmarking results. Accurate models of protein tertiary structures are now available from numerous advanced prediction methods, although the accuracy of each method often varies depending on the specific protein target. Additionally, many models may still contain significant local errors. Therefore, reliable, independent model quality estimates are essential both for identifying errors and selecting the very best models for further biological investigations. ModFOLD9 is a leading independent server for detecting the local errors in models produced by any method, and it can accurately discriminate between high-quality models from multiple alternative approaches. ModFOLD9 incorporates several new scores from deep learning-based approaches, leading to greatly improved prediction accuracy compared with earlier versions of the server. ModFOLD9 is continuously independently benchmarked, and it is shown to be highly competitive with other public servers. ModFOLD9 is freely available at https://www.reading.ac.uk/bioinf/ModFOLD/.