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Nucleic Acids Research, 2003, Vol. 31, No. 13 3349-3351
© 2003 Oxford University Press

MolSurfer: a macromolecular interface navigator

Razif R. Gabdoulline*,1, Rebecca C. Wade1,2 and Dirk Walther3

1 European Media Laboratory (EML), Schloss-Wolfsbrunnenweg 33, D-69118, Heidelberg, Germany 2 European Molecular Biology Laboratory (EMBL), Meyerhofstr. 1, D-69117, Heidelberg, Germany 3 Incyte Genomics, Inc., 3160 Porter Drive, Palo Alto, CA 94304, USA

*To whom correspondence should be addressed. Tel: +49 6221 533 266; Fax: +49 6221 533 298; Email: razif.gabdoulline{at}eml.villa-bosch.de

We describe the current status of the Java molecular graphics tool, MolSurfer. MolSurfer has been designed to assist the analysis of the structures and physico-chemical properties of macromolecular interfaces. MolSurfer provides a coupled display of two-dimensional (2D) maps of the interfaces generated with the ADS software and a three-dimensional (3D) view of the macromolecular structure in the Java PDB viewer, WebMol. The interfaces are analytically defined and properties such as electrostatic potential or hydrophobicity are projected on to them. MolSurfer has been applied previously to analyze a set of 39 protein–protein complexes, with structures available from the Protein Data Bank (PDB). A new application, described here, is the visualization of 75 interfaces in structures of protein–DNA and protein–RNA complexes. Another new feature is that the MolSurfer web server is now able to compute and map Poisson–Boltzmann electrostatic potentials of macromolecules onto interfaces. The MolSurfer web server is available at http://projects.villa-bosch.de/mcm/software/molsurfer.


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