A Guide for Protein–Protein Docking Using SwarmDock

Abstract

Many of the biological functions of the cell are driven by protein–protein interactions. However, determining which proteins interact and exactly how they do so to enable their functions, remain major research questions. Functional interactions are dependent on a number of complicated factors; therefore, modeling the three-dimensional structure of protein–protein complexes is still considered a complex endeavor. Nevertheless, the rewards for modeling protein interactions to atomic level detail are substantial, and there are numerous examples of how models can provide useful information for drug design, protein engineering, systems biology, and understanding of the immune system. Here, we provide practical guidelines for docking proteins using the web-server, SwarmDock, a flexible protein–protein docking method. Moreover, we provide an overview of the factors that need to be considered when deciding whether docking is likely to be successful.