Abstract
The CABS model can be applied to a wide range of protein-protein and protein-peptide molecular modeling tasks, such as simulating folding pathways, predicting structures, docking, and analyzing the structural dynamics of molecular complexes. In this work, we use the CABS-dock tool in two diverse modeling tasks: 1) predicting the structures of amyloid protofilaments and 2) identifying cleavage sites in the peptide substrates of proteolytic enzymes. In the first case, simulations of the simultaneous docking of amyloidogenic peptides indicated that the CABS model can accurately predict the structures of amyloid protofilaments which have an in-register parallel architecture. Scoring based on a combination of symmetry criteria and estimated interaction energy values for bound monomers enables the identification of protofilament models that closely match their experimental structures for 5 out of 6 analyzed systems. For the second task, it has been shown that CABS-dock coarse-grained docking simulations can be used to identify the positions of cleavage sites in the peptide substrates of proteolytic enzymes. The cleavage site position was correctly identified for 12 out of 15 analyzed peptides. When combined with sequence-based methods, these docking simulations may lead to an efficient way of predicting cleavage sites in degraded proteins. The method also provides the atomic structures of enzyme-substrate complexes, which can give insights into enzyme-substrate interactions that are crucial for the design of new potent inhibitors.