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The protein-protein interactions (PPIs) are crucial for understanding themajority of cellular processes. PPIs play important role in gene transcriptionregulation, cellular signaling, molecular basis of immune response and more.Moreover, a disruption of hese mechanisms is frequently postulated as apossible cause of diseases such as Alzheimer's or cancer. For many ofbiologically relevant cases the structure of protein-protein complexes remainunknown. Therefore computational techniques, including molecular docking, havebecome a valuable part of drug discovery pipelines. Unfortunately, none of thewidely used protein-protein docking tools is free from serious limitations.Typically, in docking simulations the protein flexibility is either completelyneglected or very limited. Additionally, some knowledge of the approximatelocation and/or the shape of the active site is also required. Such limitationsarise mostly from the enormous number of degrees of freedom of protein-proteinsystems. In this paper, an efficient computational method for protein-proteindocking is proposed and initially tested on a single docking case. The proposedmethod is based on a two-step procedure. In the first step, CABS-dock webserver for protein-peptide docking is used to dock a peptide, which is theappropriate protein fragment responsible for the protein-protein interaction,to the other protein partner. During peptide docking, no knowledge about thebinding site, nor the peptide structure, is used and the peptide is allowed tobe fully flexible. In the second step, the docked peptide is used in thestructural adjustment of protein complex partners. The proposed method allowedus to obtain a high accuracy model, therefore it provides a promising frameworkfor further advances.

Towards protein-protein docking with significant structural changes using CABS-dock