After docking the ligand to the protein model using Autodock, how does one identify the protein residues interacting with the ligand?
Use Ligplot software (Written by Andrew Wallace and Roman Laskowski) , it converts the 3D image to 2D image, hence all intraction between ligand and protein could be identified very easily . Please see the link below
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
If you will be using VLife MDS 4.3, then in its biopredicta tools, Vlife has provided an option to analyze interactions between best poses of ligands with amino acid residues of proteins.
Regards,
Rajeev K Singla
SERB-Young Scientist
http://rajeevksingla.in
Thanks Haresh , I have finding the residues forming polar contacts through pymol but I was looking for a better option.
Hi Rajeev,I have not used it before.Is it available for free? From where can we download it? Thanks
http://autodock.scripps.edu/downloads/autodock-registration/autodock-4-2-download-page/
Use Ligplot software (Written by Andrew Wallace and Roman Laskowski) , it converts the 3D image to 2D image, hence all intraction between ligand and protein could be identified very easily . Please see the link below
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
Dear Dr. Prerna, VLife MDS 4.3 is not a freeware. But you can request company to provide you trial for a week. I am having this software. In case, you wish to collaborate with me, but officially only with prior approval from your senior. Then I can help you to analyze the same. Mail me at [email protected] .
Poseview also works better for polar interactions and also for hydrophobic interactions
AutoMap will do this. It is published in JMGM 2013 ans is freely available on scorceforge.
Hello.
I must agree with Rahul, LIGPLOT is a great peace of software. And very simple to use.
Best regards,
Ricardo Ferreira
Hello.
STITCH:
STITCH is a resource to explore known and predicted interactions of chemicals and proteins.
http://stitch.embl.de/
LPCSU
Ligand-Protein Contacts & Contacts of Structural Units.
http://bip.weizmann.ac.il/oca-bin/lpccsu
LIGPLOT:
Program for automatically plotting protein-ligand interactions.
http://www.ebi.ac.uk/thornton-srv/software/LIGPLOT/
SuMo:
SuMo allows you to screen the Protein Data Bank (PDB) for finding ligand binding sites matching your protein structure or inversely, for finding protein structures matching a given site in your protein. This method is neither based on aminoacid sequence nor on fold comparisons.
http://sumo-pbil.ibcp.fr/cgi-bin/sumo-welcome
Ligplot for 2D interactions and Molegro molecular viewer, Chimera, VMD for viewing interaction in 3D.
Thanks Ramanuj. Can you do 2D representation with Pymol or chimera..?
Also you can use Accelerys DS Visualiser to see the interactions between them
Use pymol, for example, and this command:
select (name selection that you want), protein within (distance) of ligand
This show you the amino acids araund a distance x of the ligand
I would suggest you to go with Autodock/Vina plugin for PyMOL http://wwwuser.gwdg.de/~dseelig/adplugin.html
is it possible with LigPLOT (if I upload pdb file of the protein and 10 binding modes of 10 ligands, all in one or two file) to search for the number/percentage of polar interactions, non polar interactions, hydrogen interactions? Is it possible to get it as an output?
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