Section: Application Domains
Keywords : Molecular dynamics.
Protein docking is a fundamental biological process that links two proteins. This link is typically defined by interactions between two large zones of the protein boundaries. Visualizing the interfaces where these interactions take place is useful to understand the process thanks to 3D protein structures, to estimate the quality of docking simulation results, and to classify interactions in order to predict docking affinity between classes of interacting zones. Our developments take place in the VMD software (in cooperation with ORPAILLEUR and the Beckmann Institute at University of Illinois). More recently, in the frame of his Ph.D., Matthieu Chavent studied new means of visualizing molecular surfaces, which play an important role in better understanding the nano-scale mechanisms of life.