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.
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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.