Protein-protein and peptide-protein docking and refinement using ATTRACT in CAPRI

Proteins, DOI: 10.1002/prot.25196
Proteins, online article

The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28–36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success rate of 67%. In particular, for several peptide-protein complexes excellent predictions were achieved. In several cases, a combination of template-based modeling and extensive molecular dynamics-based refinement yielded medium and even high quality solutions. In one particularly challenging case, the structure of an ubiquitylation enzyme bound to the nucleosome was correctly predicted as a set of acceptable quality solutions. Based on the experience with the CAPRI targets, new interface refinement approaches and methods for ab-initio peptide-protein docking have been developed. Failures and possible improvements of the docking method with respect to scoring and protein flexibility will also be discussed.

TU München
Helmholtz München
MPI of Neurobiology
MPI of Biochemistry