Interactive Poster: Visualizing the Interaction Between Two Proteins

Nicolas Ray (1) , Xavier Cavin (1) , Bernard Maigret

1 ISA - Models, algorithms and geometry for computer graphics and vision

Protein docking is a fundamental biological process that links two proteins in order to change their properties. The link is defined by a set of forces between two large areas of the protein boundaries. Two docked proteins are very close to each other due to the VdW forces. This makes the understanding of the phenomenon difficult using classical molecular visualization. We present a way to focus on the most interesting area: the interface between the proteins. Visualizing the interface is useful both to understand the process thanks to co-crystallized proteins and to estimate the quality of docking simulation result. The interface may be defined by a surface that separates the two proteins. The geometry of the surface is induced by the VdW forces, while other forces can be represented by attributes mapped onto the surface. We present a very fast algorithm that extracts the interface surface. Moreover, the result of a rigid docking simulation can be improved using the flexibility of the residues. We show how the interface surface geometry and attributes can be updated in real-time when the user interactively moves the residues. This way, we allow expert knowledge to be intuitively introduced in the process to enhance the quality of the docking.

Mots clés: protein docking; docking proteines

Domaines: Autre [cs.OH]

Nicolas Ray, Xavier Cavin, Bernard Maigret. Interactive Poster: Visualizing the Interaction Between Two Proteins. IEEE Visualization 2003, 2003, Seattle, United States. ⟨inria-00107708⟩