Interactive Analysis and Visualization of Macromolecular Interfaces between Proteins

Molecular interfaces between proteins are of high importance for understanding their interactions and functions. In this paper protein complexes in the PDB database are used as input to calculate an interface contact matrix between two proteins, based on the distance between individual residues and atoms of each protein. The interface contact matrix is linked to a 3D visualization of the macromolecular structures in that way, that mouse clicking on the appropriate part of the interface contact matrix highlights the corresponding residues in the 3D structure. Additionally, the identified residues in the interface contact matrix are used to define the molecular surface at the interface. The interface contact matrix allows the end user to overview the distribution of the involved residues and an evaluation of interfacial binding hot spots. The interactive visualization of the selected residues in a 3D view via interacting windows allows realistic analysis of the macromolecular interface.

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