Protein Model Quality - Part 1: Exploring AlphaFold's pLDDT scores in 2D and 3D views in Jalview

Learn how users can visualise and interact with AlphaFold's pLDDT score in Jalview by selecting, hiding and applying shading to various regions of the alignment. Jalview allows mapping and manipulation of structures in other 3D molecular graphics viewers including ChimeraX, UCSF Chimera and JMol in a similar way. 0:00 Why is protein model quality important? 1:32 Searching the 3D Beacons network from Jalview 3:02 Loading pLDDT scores 3:52 Enlarging pLDDT scores 4:13 Interpreting pLDDT scores 4:40 Colouring sequences using one pLDDT score 6:14 Colouring sequences using individual pLDDT scores 6:39 Colouring sequences by pLDDT score threshold 7:35 Selecting sequence columns by pLDDT score 8:32 Hiding sequence columns by pLDDT score Produced by Khadija Jabeen for the University of Dundee. With support from Professor Geoffrey J. Barton and Dr. James Procter. Funding from the Biotechnology and Biological Sciences Research Council (Grant number: BB/X018628/1) and the Wellcome Trust (Grant number: 218259Z/19/Z) is gratefully acknowledged. Download Jalview: https://www.jalview.org/download/ Enlargement or minimisation of the pLDDT reference annotation track in Jalview, as demonstrated in this video, may be achieved by click-dragging on the plot, in the up or down direction. (This work is licensed under the Creative Commons Attribution 4.0 International License)