Assessment of protein assembly prediction in CASP13

TL;DR

This paper evaluates the progress and challenges in predicting protein assemblies in CASP13, highlighting increased participation, modest improvements, and the importance of considering oligomeric states for accurate modeling.

Contribution

It provides an assessment of the assembly prediction category in CASP13, emphasizing the need for integrated approaches that incorporate multiple subunits.

Findings

Increased participation and more oligomeric targets compared to previous CASP.

Ignoring oligomeric states hampers tertiary structure prediction accuracy.

Some groups successfully predicted interfacial contacts, but did not incorporate them into assembly models.

Abstract

We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake in participation, more oligomeric targets released, and consistent, albeit modest, improvement of the predictions quality. Looking at the tertiary structure predictions we observe that ignoring the oligomeric state of the targets hinders modelling success. We also note that some contact prediction groups successfully predicted homomeric interfacial contacts, though it appears that these predictions were not used for assembly modelling. Homology modelling with sizeable human intervention appears to form the basis of the assembly prediction techniques in this round of CASP. Future developments should see more integrated approaches to modelling where multiple subunits are a natural part of the modelling process, which would benefit the structure prediction field as a whole.