Assessment of the CASP14 Assembly Predictions

By Burcu Ozden, Andriy Kryshtafovych, Ezgi Karaca. 2021

39 citations recorded by the source corpus.

In CASP14, 39 research groups submitted more than 2500 3D models on 22 protein complexes. In general, the community performed well in predicting the fold of the assemblies (for 80% of the targets), although it faced significant challenges in reproducing the native contacts. This is especially the case for the complexes without whole‐assembly templates. The leading predictor, BAKER‐experimental, used a methodology combining classical techniques (template‐based modeling, protein docking) with deep learning‐based contact predictions and a fold‐and‐dock approach. The Venclovas team achieved the runner‐up position with template‐based modeling and docking. By analyzing the target interfaces, we showed that the complexes with depleted charged contacts or dominating hydrophobic interactions were the most challenging ones to predict. We also demonstrated that if AlphaFold2 predictions were at hand, the interface prediction challenge could be alleviated for most of the targets. All in all, it is evident that new approaches are needed for the accurate prediction of assemblies, which undoubtedly will expand on the significant improvements in the tertiary structure prediction field.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Andriy Kryshtafovych
2. Torsten Schwede
3. Yang Zhang
4. Krzysztof Fidelis
5. John Moult
6. Jeffrey J. Gray
7. Jianlin Cheng
8. Kliment Olechnovic

In Molecular Biology

1. Andriy Kryshtafovych
2. Yang Zhang
3. Torsten Schwede
4. Krzysztof Fidelis
5. John Moult
6. Björn Wallner
7. Jeffrey J. Gray
8. Shengyou Huang

Citations in the corpus

• Assessment of three-dimensional RNA structure prediction in CASP15 (2023, neutral): “Inspired by prior joint assessments by CAPRI and CASP for protein complexes (see References 15 – 19), two assessments were carried out for RNA: one assessment was performed by the RNA-Puzzles team (Z. Miao & E. Westhof) and a completely independent analysis was performed by assessors nominated by…”
• Critical Assessment of Methods of Protein Structure Prediction (CASP) – Round XIV (2021, methodology): “complexes, with two corresponding assessment papers.(3,4) Thirty-nine groups took part in this modeling category, with 22 targets altogether, 12 of which were also considered by CAPRI participants.”
• Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment (2021, background): “also included, but will only briefly discussed, since their performance is evaluated in a separate publication.(45) Values of all the CAPRI quality assessment measures for individual models submitted by CAPRI participants for the 12 Round 50 targets have been communicated to the”
• Cryo-EM targets in CASP14 (2021, unknown): “accuracy of the individual protein level predictions, the prediction of quaternary structures was not successful, possibly due to the size and complexity of those assemblies.(7)”
• CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, background): “While AlphaFold2 did not participate in the assembly category in CASP14, it was noted that its predictions could have alleviated many interface modeling errors 4 .”