Molecular and Cellular Modeling Group
a Macromolecular Interface Navigator
Please note our new molsurfer implementation at This page is only kept for reference and for downloading the old version.
You will not be able to launch jobs on this site any longer.

MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures.
It is a Java-based software that uses the representation of the macromolecular interface generated by adsi (the interface module of ads, analytically defined molecular surfaces ) and  WebMol, a Java-based PDB viewer .

MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces.  The 2D projections of the computed interface aid visualization of complicated interfacial geometries in 3D. Molecular properties, including hydrophobicity and electrostatic potential, can be projected onto the interface. MolSurfer can thereby aid exploration of molecular complementarity, identification of binding "hot spots" and prediction of the effects of mutations. MolSurfer can also facilitate the location of cavities at macromolecular interfaces.

Running MolSurfer

MolSurfer can be run as an applet or as a stand alone program.

MolSurfer Tutorial
  • Investigate the distribution of the electrostatic potential on a protein-protein interface by following step-by-step instructions
  • MolSurfer Servers
    MolSurfer Demos
    MolSurfer web server 
    • Submit the coordinates of 2 interacting macromolecules (protein/dna/rna) in PDB format
    • Electrostatic properties are not computed
    Protein-protein demo 
    • Investigate preprocessed 39 protein-protein interfaces
    MolSurfer web server with electrostatic calculations 
  • Submit the coordinates of 2 interacting macromolecules (protein/dna/rna) in PQR format
  • Electrostatic properties will be computed, and this may take up to 1 minute
  • Protein-dna/rna demo 
    • Investigate preprocessed 75 protein-dna/rna interfaces

    Additional demo
    P450 substrate exit pathway demo 
    • Investigate trajectories from molecular dynamics simulations of substrate egress from the active site of cytochrome P450. For detailed description, see: the reference or this website

  • Indira Shrivastava  for her contribution to preparing the set of protein-protein complexes;
  • Susanna Luedemann  for her permanent interest in MolSurfer;
  • David Goodsell for an comment that triggered the idea to link 2D and 3D.

  • References

  • R.R. Gabdoulline, R.C. Wade & D. Walther (2003) MolSurfer: a macromolecular interface navigator, Nucleic Acids Research, 31, 3349-3351. abstract and full text
  • R.R. Gabdoulline, R.C. Wade & D. Walther. (1999) MolSurfer: two dimensional maps for navigating three-dimensional structures of proteins, Trends Biochem. Sci., 24, 285-287 . (excerpt)
  • Application Examples

  • Hough MA, Hall JF, Kanbi LD, Hasnain SS. (2001) Structure of the M148Q mutant of rusticyanin at 1.5 angstrom: a model for the copper site of stellacyanin, Acta Crystallogr D, 57, 355-360.
  • Luedemann SK, Gabdoulline RR, Lounnas V, Wade RC, Substrate access to cytochrome P450cam investigated by molecular dynamics simulations: An interactive look at the underlying mechanisms,  Internet. J. Chem. (2001) 4, 6.  (abstract)
  • Campbell JD, Biggin PC, Baaden M, Sansom MSP (2003) Extending the structure of an ABC transporter to atomic resolution: Modeling and simulation studies of MsbA, Biochemistry, 42 (13), 3666-3673.
  • Flaus A, Rencurel C, Ferreira H, Wiechens N, Owen-Hughes T (2004) Sin mutations alter inherent nucleosome mobility, EMBO Journal, 23, 343-353.
  • Wang T, Tomic S, Gabdoulline RR, Wade RC (2004) How optimal are the binding energetics of barnase and barstar? Biophys J. 87, 1618-30.
  • Huelsmeyer M, Chames P, Hillig RC, Stanfield RL, Held G, Coulie PG, Alings C, Wille G, Saenger W, Uchanska-Ziegler B, Hoogenboom HR, Ziegler A, (2005) A Major Histocompatibility Complex Peptide-restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes (A Major Histocompatibility Complex Peptide-restricted Antibody and T Cell Receptor Molecules Recognize Their Target by Distinct Binding Modes), J. Biol. Chem. 280, 2972-2980.
  • Kövesi I, Schay G, Yonetani T, Laberge M, Fidy J, (2005) High pressure reveals that the stability of interdimeric contacts in the R- and T-state of HbA is influenced by allosteric effectors: Insights from computational simulations, Biochim Biophys Acta, 1764, 516-21.

  • Authors

    Rebecca Wade,
    HITS gGmbH, Schloss-Wolfsbrunnenweg 35,  D-69118 Heidelberg, Germany,
    European Molecular Biology Laboratory (EMBL), Meyerhofstr 1,  D-69012 Heidelberg, Germany,
    Dirk Walther
    Incyte Genomics, Inc, 3169 Porter Drive, Palo Alto, CA 94304, USA

    (c) 1999, 2003

    R. Gabdoulline, Fri 04 Apr 2003 Imprint/Privacy