PLATINUM is designed for calculation of hydrophobic properties of molecules and their match or mismatch in receptor–ligand complexes. These properties may help to analyze results of molecular docking.

Step 1: Upload files

Select “ligand” file(s) — to view their hydrophobic properties; add a single “receptor” file to assess the hydrophobic complementarity between them. If “receptor” is a lipid bilayer or an α-helix, 2D hydrophobicity maps can be calculated for it. (File size limit: 5 Mb.)

Please note: If Adobe Flash 9 (not 10th!) is not installed then use simple upload mode.

Receptor:


Ligand(s):

Please note: Explicit hydrogens required!

What is PLATINUM?

Calculate and visualize molecular hydrophobic/hydrophilic properties using the concept of “Molecular Hydrophobicity Potential” (MHP). Hydrophobic and stacking interactions in biomolecular complexes can be estimated and used to re-rank the results of molecular docking. For certain cases — lipid bilayers and α-helices — 2D hydrophobicity maps can be calculated.

How to use PLATINUM?

  • Complementarity of hydrophobic/hydrophilic properties in biomolecular complexes:
    • to view molecular hydrophobic properties upload ligand(s);
    • to view hydrophobic complementarity add a receptor;
    • on Step 2 select a reference ligand (optionally).
  • 2D hydrophobic maps for lipid bilayers and α-helices:
    • upload a bilayer or an α-helix as a receptor (currently only.GRO files are allowed);
    • add ligand(s) to view the contact area on the map (optionally).

For details refer to the manual and go through the tutorial; don’t forget files for the tutorial.

System requirements

Some components on the site (viz. massive files upload) require modern web-browser with javascripts enabled and Flash-9 plugin installed. You’ll also need Java to see visualization online.