Assessment of protein assembly prediction in CASP13

By Dmytro Guzenko, Aleix Lafita, Bohdan Monastyrskyy, Andriy Kryshtafovych, Jose M. Duarte. 2019

39 citations recorded by the source corpus.

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 modeling 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 modeling. Homology modeling 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 where subunits are modeled in the context of the assemblies they form.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Cryo-EM targets in CASP13: overview and evaluation of results (2019, result): “Similar to the outcome of the tertiary structure analysis, the results on the quaternary structure for cryo-EM targets are similar to the results for the complete set of all CASP13 targets.(2)”
CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods (2021, unknown): “12 The oligomeric lDDT score (oligo-lDDT) is an extension of the lDDT score for protein complexes and has also been used in CASP since CASP13.”
Assessment of the CASP14 Assembly Predictions (2021, methodology): “The Seok-naïve-assembly predictions have been used as a reference to assess the homomeric predictions since the earlier CASP rounds.(11) In CASP14, all the topperforming groups produced better quality models than the Seoknaïve-assembly (Figure S6).”