Would you embark on a hike without a map
or a guide? Ever felt lost in the forest of amino acids as you explored
a protein structure on a graphics workstation? The complexity of
interfaces between proteins in protein assemblies can be daunting.
Like the hiker, you need a map to help you navigate. We have therefore
produced MolSurfer, a tool that provides two-dimensional (2D) maps of protein
interfaces that can be used to explore three-dimensional (3D) structures
of protein complexes and their interfaces.
We developed MolSurfer to facilitate studies of intermolecular interactions between proteins. MolSurfer is a graphical tool that links a 2D projection of a protein-protein interface to a 3D view of the protein structures. This Java-based software uses the representation of the protein protein interface generated by ADSI, the interface-mapping module of the ADS (analytically defined surfaces) software, and WebMol, a Java-based PDB viewer. The interface comprises two linked windows. The first window, MolSurfer, displays 2D maps computed by ADSI that display molecular properties (such as intermolecular separation, hydropho-bicity and electrostatic potential), are projected onto the interface. The second window, WebMol, displays 3D representations of the molecules. The two windows are linked in such a way that mouse manipulations on the 2D-map window change the map and the 3D view. This link allows researchers to use a 2D map to navigate in a 3D view. MolSurfer is applicable to in-depth study of pairs of molecules or large-scale analyses of sets of structures, such as a database of different protein-protein complexes (see below) or a set of mutants of one protein-protein complex.
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