Out of topic: Plot Ligand-protein interactions

From: Kimi
Date: 20 January 2012 07:46

Dear all,

I would like to know what program/software you usually use to plot the 2D interactions between ligand and protein. As far as I know, LigPlot is powerful but need some skills. Also a web-based program from PDB server is easy to use but not very powerful.

What is your recommendation? Thank you.

King regards,
Wenhe

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From: krish


Dear Wenhe,

You don't need any skills to use Ligplot. Only thing you have to give is the "residue number" of the ligand or the small molecule you are interested in the command line.

There are other commercial software but i don't know whether they are of any interest to you ! MOE  or  MAESTRO  also provides 2D plotting.

HTH !

Regards,

Krishna Chinthalapudi, PhD
Hannover Medical School

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From: Tom Oldfield

Wenhe

There is a ligand environment viewer at the URL below that plots environments of ligands
in various view types.  At the moment is only works on existing structures since the ligands
have to be correctly typed with correct dictionaries.

This has a number of export formats.

http://www.ebi.ac.uk/pdbe-srv/leview/

The EBIAstexViewer
http://www.ebi.ac.uk/pdbe-srv/view/entry/1cbs/viewer

Also has a chemistry viewer (menu -> Chemistry) which shows the ligand in 2D with the
environment and various options.  You asked for plotting - so I guess you want an export
format so I am not sure if this is suitable.

Regards
Tom Oldfield