I have docked two proteins using Patchdock tool and firedock. How will I point out those amino acids which are involved in binding of the two proteins, using which software?
If you can obtain ligand+protein (docked) complex in .pdb format, you can submit that structure in PDBsum (www.ebi.ac.uk/pdbsum/) to see the amino acids involved in hydrogen bond and hydrophobic interaction
Thanks. But I predicted the protein, it is not there in PDB. The site is asking for PDB code.
Use LigPlot+ (http://www.ebi.ac.uk/thornton-srv/software/LigPlus/). It is free for academic use. All the interaction diagrams in PDBe are made with this software.
In this software you can visualize both the small molecule-protein interface (LIGPLOT) as well as protein-protein interface (DIMPLOT) in two and three dimensions (using RasMol and PyMOL plug-in).
For protein-small molecule interactions you may also use PoseView server (http://poseview.zbh.uni-hamburg.de/). All the RCSB PDB ligand interaction diagrams are made with this software.
Use this link, which gives you every interaction possible.........
http://nucleix.mbu.iisc.ernet.in/nbif/index.php
give your feedback also
Its still in testing period (not yet published, but I think it can serve the purpose)
You can contact me for further queries....
Thanx alot
Go for any 3-d viewer and separate them in different colour, it will visualize the amino acids.
As Mousami correctly hints, you couls load the molecules into Pymol and use the cmd.dist() function in a simple Python script that will color all pairs of amino-acids from two proteins that fall below some distance threshold. The script will most likely have a dozen lines or so, iterating over all possible pairs and testing C-alpha distances or a similar measure, calling cmd.color() on those that pass the test. I found an old script that iterated over C alpha atoms for a different purpose (coloring amino acids according to the distance/number of neighboring residues) that could give you some ideas.
Hi, there are a lot software able to perform this calculation. Ligplot is very good, but if you have Maestro Schrodinger suite (the graphical interface is free for academics) you can use ligand interaction diagram from toolbar or you can install the script Ligand interaction diagram 3D and the interactions between ligand and the protein are displayed in 3D; this tool is very very nice. Moreover, I have used an online tool named poseview: http://poseview.zbh.uni-hamburg.de/ ..... it works very well!!!!
You can use online Ligplot tool which is incorporated in PDBsum (EBI), you can get the stand alone version of this Ligplot which has described earlier. Apart from them you can use PoseView which can also detect the various kinds of intercation between receptor and ligands. You can also use the HBAT (Hydrogen Bond Analysis Tool) which is also requires a simple protein-ligand complex in pdb format.
you can use PLIP: fully automated protein–ligand interaction profiler. Its a fully automated and easy to use. And LIGPLOT also will be the best if you get the academic licence otherwise go for PLIP.
you can use the following tool:
http://bioinf.modares.ac.ir/software/cfinder/
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