R.R. Gabdoulline, R.C. Wade & D. Walther
MolSurfer: two dimensional maps for navigating three-dimensional structures of proteins
Trends Biochem. Sci., 24, 285-287

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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