Hello everyone, I need to dock siRNA with a peptide. Both siRNA and peptide (9-20 amino acids) were minimized with NAMD prior to docking. What I did was extract the coordinates from the last frame and uploaded to ClusPro. Can someone tell me why it gives "Unknown residue GUA in receptor. Please remove." error? Thank you
Just checking what ClusPro is, and turns out it is a protein-protein docking tool. GUA here refer to guanine residue, in case of protein-protein docking tool I think no polynucleotide will be recognized, not only guanine, but also adenine, cytosine, thymine/uracil. In my opinion I think elucidating the binding of peptide and RNA is much better using molecular dynamics method rather than docking. Especially when you have experience with NAMD.
http://scholar.google.com/scholar?q=peptide+rna+molecular+dynamics+simulation&btnG=&hl=en&as_sdt=0%2C5
Hope that help,
Radif
hello Muhammad Radifar,
ClusPro mentioned that it accepts RNA, but only as the receptor, so it should accept RNA. and thank you very much for your idea Radif!
Hmm... interesting.
I just checked again the website and you're right, and I found something interesting (if you still would like to continue using docking). Check this out:
http://cluspro.bu.edu/rna.php
Turns out that for every residue of RNA should be replaced with one letter. I think you have to manually change the residue name using any text editor of your choice, and use "Find and replace" feature to change all of the four residue to its corresponding one letter residue.
Good luck!
already i tried that Radifar, changing the three letter notation to single letter breaks the whole structure. now im looking for ATOM and HETATOM formated PDBs..
That's most probably caused by the very strict PDB column rule (http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/framepdbintro.html). I forgot to mention that the 3 character should be replaced by 3 character as well. For example from "GUA" --> "G ", you need to add 2 more space behind G.
Exactly!! i used http://sourceforge.net/projects/pdbeditorjl/ to edit PDB and just now knew about the two space thing. thank you very much Radifar, now its work like a charm...
Great! I usually use either Notepad++ or sed (terminal-based built-in program in Linux) to make such editing. In Notepad++ the find and replace feature able to replace with additional space character, which is very useful in many occasion.
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