The goal of CASP experiments is to monitor the progress in the protein
structure prediction field. During the 14th CASP edition we aimed to
test our capabilities of predicting structures of protein complexes. Our
protocol for modeling protein assemblies included both template-based
modeling and free docking. Structural templates were identified using
sensitive sequence-based searches. If sequence-based searches failed, we
performed structure-based template searches using selected CASP server
models. In the absence of reliable templates we applied free docking
starting from monomers generated by CASP servers. We evaluated and
ranked models of protein complexes using an improved version of protein
structure quality assessment method, VoroMQA, taking into account both
interaction interface and global structure scores. If reliable templates
could be identified, generally accurate models of protein assemblies
were generated with the exception of an antibody-antigen interaction.
The success of free docking mainly depended on the accuracy of initial
subunit models and on the scoring of docking solutions. To put our
overall results in perspective, we analyzed our performance in the
context of other CASP groups. Although the subunits in our assembly
models often were not of the top quality, these models had, overall, the
best predicted interfaces according to several protein-protein interface
accuracy measures. Since we did not use co-evolution-based prediction of
inter-chain contacts, we attribute our relative success in predicting
interfaces primarily to the emphasis on the interaction interface when
modeling and scoring.
Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study
