Dear all,
I want to identify pi-pi base stacking interactions between my ligand and DNA. How can I do this using PyMOL? Can anyone help me?
Thank you in advance.
You can probably find your answer in the following link: (http://www.pymolwiki.org/index.php/Ideas)
Alternatively, pi-pi or other weak interactions and their all quantitative details also can be calculated for your system through ORTEP-PLATON program. You may try that too.
Although not directly related to your requirement (DNA and Ligand), if you are interested in analyzing pi-pi interaction and interaction network within a protein, then iCAPS module of iRDP (http://irdp.ncl.res.in) server might be useful.
With iCAPS (in silico comparative analysis of protein structures), one can compare at most 100 protein structures simultaneously with respect to differences in aromatic-aromatic residue interaction networks present among them.
Besides aromatic-aromatic interactions, one can also compare other structural features.
Thanks
We have developed a program called MolBridge (http://nucleix.mbu.iisc.ernet.in/molbridge/index.php)....U can try dis, where we give the area overlap also....
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