A program for finding non-bonded interactions in small molecule and biomolecule structures

Please let the cursor hover over the option headers for hints.

MolBridge is a program to automate the analysis of potential hydrogen bonds and other important weak interactions like halogen bonds and non-canonical interactions in small molecule as well as biomolecular structures. Reduce program is used to add hydrogen atoms for biomolecules in PDB format, while Open Babel is used for small molecules and other non-PDB formatted input files. MolBridge identifies potential interactions based on geometrical criteria and can be used to analyze active site interactions, structure based drug design and molecular dynamics simulations. This web server version of MolBridge uses JmolApplet to display the molecules and the respective interactions.

The web server uses Jmol (Java applet) and hence the web browser must have latest JAVA installed and the Java applets enabled.

Molecule Type:

Small molecule Biomolecule                 


ID for Small Molecule:

  Please select the database and enter the small molecule ID:

COD         CSD         Pubchem
  Enter ID here:


ID for Biomolecule:

  Please enter 4 letter PDB-ID:

------ or ------

Upload a File
  (Please enter the file format type in the appropriate box):

  You can upload a file containing atomic coordinates:

  Please enter the input file format type:    (default type is pdb)


Calculation of symmetry related interactions   (only for small molecules):

Not required
Use symmetry information provided in the file
Input the symmetry informations below

        symmetry information will not be used.


For Drawing Molecule Using JME:




Does input file have hydrogen atom co-ordinates?

Yes              No


van der Waals Interactions:

 van der Waals Interactions   


Algorithm Parameters

  Please select the parameters




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