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CAPRI communitywide experiment on the comparative evaluation of protein-protein docking for structure prediction

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CAPRI Assessment results

Round 54 CASP15-CAPRI

CAPRI Round 54 comprised 37 targets, divided into 38 Assessment Units (AU). The assessment results of the top-5 submitted models for Predictors, Scorers, and CASP Assembly Prediction participants for all individual target interfaces are collected in this comma-separated file. For explanation of the invididual columns we refer to the CAPRI Scoreset v2022 help page.

Most AUs are single-target single-interface, with the exception of the following:

Target AU 1 AU 2
T203 average of interfaces 1-3 interface 4
T204 best of interfaces 1-2 average of interfaces 3-8
T219/T220/T221 best of interfaces 1-3 best of interfaces 4

You can find the slides of Marc Lensink’s CAPRI presentation in the CASP assembly session HERE.

The image below shows the CAPRI ranking. “AF2-MULTIMER” is the off-the-bench AlphaFold-Multimer modeling as submitted by the Elofsson group.

Round 53 Target T187 and T188

Targets T187 and T188 featured a large conformational change upon binding to dsDNA. However, the AlphaFold monomer structure captured this conformational change perfectly. Unfortunately, no predictors or scorers were able to produce acceptable models for T187. The assessment results for the top-5 submitted models are collected in this comma-separated file. In this file, interface 1 corresponds to the whole target; interface 2 is the protein dimer alone.

For T188 the bound dsDNA structure was given. This resulted in acceptable models for 2 predictor groups: Fernandez-Recio (top-1) and Pierce (top-5); and 5 scorer groups: Fernandez-Recio, Zou and server PYDOCKDNAWEB (top-1), and Kihara and server MDOCKPP (top-5).

Medium-quality models for the protein dimer were produced (in top-5 submission) by Venclovas, Zacharias, Huang, Chang, Kihara, and servers LZERD and HDOCK. Scorers Kihara, Bates, Huang, Chang, Zou, Shen, and servers HDOCK, LZERD and PYDOCKDNAWEB recognized these (again, top-5).

The quality of the protein-dnDNA models strongly depended on the protein dimer modelling quality, as can be seen in the image below.

For questions or comments please contact Marc Lensink