Hello everyone,
I have a problem regarding the performance of a docking calculation between a large polymer and a protein. The polymer is really huge.
I have tried vina and autodock, but the polymer has more than 32 rotable bonds. Additionally I have tried other softwares like Rosetta or HEX, but with not succes, because are prepared for small molecules.
Any advice or possible solution?
Thanks in advance,
Best regards,
Hi you can try GOLD software. It has not problems concerning the number of rotatable bonds. In addition, you can try Bioluminate suite 2015 distributed by Schrodinger in which the maximum rotatable bonds was set to 50 by using Glide docking program.
Sincerely
Thanks for your answers.
SwissDock seems that is not working, due to size problems, as with other software tools.
On the other side, I don't know hot to download Gold. Can you help me with that?
Bioluminate maybe is an option but I can only obtain a trial version right? I prefer something more "stable working".
Thanks
Hi, unfortunately the mentioned programs are not free. probably you can obtain a trial version of them. GOLD is distributed by CCDC (cambridge crystallographic data centre) at this link http://www.ccdc.cam.ac.uk/SupportandResources/Downloads/pages/ProtectedDownloadProductList.aspx. Bioluminate is distributed by schrodinger (http://www.schrodinger.com/).
Sincerely
Go ahead with ClusPro 2.0 (http://cluspro.bu.edu/login.php) or Haddock (http://haddocking.org/) and perform as you do for protein-protein.
There is no pride in this; but one time I managed a tolerable docking of a similar sized polymer by docking a poly-glycine "protein" chain of the same length as the polymer with some software which would only handle protein/protein associations. Followed by a Kabsch algorithm replacement of the poly-glycine ensembles by the proper polymer and then some MD to do some local relaxation. It was slow, but it provided one decent possibility, (certainly not "the solution". any time someone gives you just one "solution" you should be skeptical)
You use PatchDock server. Here you dock for protein-protein docking as well as protein-ligand docking. It will give more than 20 structures at a time. You have to analyze and you select which one will be perfect one according to requirement.
@ Melchor Sanchez-Martinez
Which one works well for protein-polymer docking?
All depends on your system and mostly its size. Seems that patchdock is a good option for dendrimers, although in my case any of them worked fine and I did long MD simulations to observe the binding.
Hi
According to CAPRI ranking, Cluspro docking web servers is giving a significantly better result among others. But you can try other softwares also like PatchDock, Rosetta-Dock, Z-Dock, Gramm-X also they also giving good result. Even in PatchDock you can refine your docking result using FireDock or FibreDock.
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