I want to study the interaction of my protein with other proteins through docking and simulation studies, etc. My desired protein is active when it is ubiquitinated. I have modeled my protein and retrieved the Ubq model from PDB. Now I am trying to create a bond between lysine of target protein and Gly of the Ubq protein. But I am unable to figure out how to do this? Is there any free tool that can create a bond as well as suggest the relative orientation of both proteins?
You may try Schrodinger Maestro academic version where you can create the desired bond useing the "build tool". Then, do a restrained minimization followed by molecular dynamics in Desmond for a short time. That should orient the protein correctly. The whole interface is very userfriendly and intuitive. They have very good tutorial as well. The academic version is free.
http://www.deshawresearch.com/resources_desmond.html
Keeping the Ubq in right orientation is the biggest problem here. You can use Modeller multiple template modeling strategy for this purpose. You have structure file of both. Consider Your protein and your Ubq as template and use a fused sequence of both as target sequence. A possible illustration of alignment file is below.
Template 1 Seq : AAAAAAAAA
Template 2 Seq : BBBBBBBB
Ali File
>P1
structure
AAAAAAAA-----------*
>P1
structure
-----------BBBBBBB*
>P1
sequence
AAAAAAAABBBBBBB*
Wishes.
Thank you Uttam Pal and R. Namdeo for such a prompt reply. I will go for Schrodinger Maestro as this suits better to my situation
You can use docking with a distance constraint between the Ub and the relevant Lys on your protein. You can try it here: http://bioinfo3d.cs.tau.ac.il/PatchDock/
Advanced options allow you to add it.
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