Similar protocols

Protocol publication

[…] the five predictions for each target may have been purposefully chosen so that they cover a larger conformational space between them, preventing the submission of five very similar but incorrect models. This indicates that the ranking method used cannot consistently choose the best conformations., The results obtained during AMA-II, as well as some other H3 prediction studies, are shown in . Reasonable accuracies are currently being achieved for short H3 loops (up to around 9 residues), but predictions become far worse for loops beyond that length. There is an appreciable difference in accuracies achieved modelling H3 loops compared to the other CDRs. For example, the knowledge-based method FREAD has been shown to produce sub-ångström predictions for the five canonical CDRs (0.81  Å, 0.42  Å, 0.96  Å, 0.98 Å and 0.88  Å for L1–H2), while the average accuracy for H3 loops is 2.25  Å . RosettaAntibody also produces sub-ångström predictions for the other CDR loops (0.78  Å, 0.54  Å, 0.81  Å, 0.84  Å and 0.93  Å), while the accuracy of H3 prediction ranges between 1.6  Å and 6.0  Å depending on length., The following sections provide details of the algorithms whose accuracy is reported in . Although the algorithms described are all H3-specific, or have been used to model H3 loops, they give an overview of the methodologies used for loop modelling in general., ABGEN (the AntiBody structure GENeration algorithm) is an antibody modelling tool published by Mandal et al. . There are two parts to the algorithm: ABalign, which selects a template structure for each part of the structure (i.e. framework and CDRs) by sequence similarity; and ABbuild, which is responsible for generating the three-dimensional structure. The CDRs are modelled using a knowledge-based approach, and the H3 loop is not treated any differently — candidate templates are found from known antibody structures and selected based on sequence and length. If no loop exists of the same length, then the closest is selected. The loops are grafted onto the framework structure by superimposing the anchor […]

Pipeline specifications

Software tools FREAD, RosettaAntibody, ABGEN