Docking double-stranded DNA to a protein

[Anonymous]

I wonder if there is an example or tutorial for DNA-protein docking. How to prepare the file? Which command and flags to use?

My dsDNA is about 20 bps, protein has about 600 Aa. I would like to find the DNA interaction surface on the protein.

Any suggestion for other software, or sharing your successful experience would be highly appreciated.

Thanks!

[Anonymous]

This _may_ get you started: http://www.rosettacommons.org/manuals/archive/rosetta3.3_user_guide/app_RosettaDNA.html

I’ve emailed some of the DNA people to get them to give ideas.

[Anonymous]

Phil Bradley tells me:

“I’m not aware of any out-of-the-box functionality implemented in trunk for doing this. We have some stuff that we are working to check in, but probably not for another release cycle or so. There are bioinformatics programs designed to find DNA binding sites based on protein sequence and structure, which might work as well as explicit DNA docking in this case.”

[Anonymous]

Dear smlewis, thank you.
I am also try to run the demo dock_ligand_and_proteins in RosettaCon2011Demos with version 3.2.1 by following the “Dock Ligand and Proteins Tutorial.txt” in the top folder of the package and I could not make it work.
(1) the “clean_pdb.py” script gives ImportError: No module named amino_acids. I have python 2.7 installed.
(2) The rap.mol file generated by Pymol1.3 from my machine has less H (~10 H less) than the file supplied in the folder Part1.
(3) “Rosetta_scripts.linuxgccrelease” does not work in the folder Part2:
ERROR: LIGAND_AREAS is not known to the DataLoaderFactory. Was it registered via a DataLoaderRegistrator in one of the init.cc files (protocols/init.cc or protocols/init.cc)?
ERROR:: Exit from: src/protocols/jd2/parser/DataLoaderFactory.cc line: 73
(4) the second paragraph of the last part “Summing up” seems confusing concerning the Part1 and Part2.
(5) This introduction from RosettaCon2011Demos seems different from the introduction part from rosetta Manual. For example the former did not mention anything about adding charges.
Thank you!

[Anonymous]

Thank you for the comments. Concerning the questions in my last post, they have nothing to do with my DNA-protein dock question. I just wanted to learn ligand-protein dock module from rosetta. I should post my questions by starting a new topic. Unfortunately, the tutorial for FKBP12, FRAP and rapamycin docking did not work for me, I think that the difficulties are not only from the version problem.

[Anonymous]

The error in part 3 is probably due to using 3.2.1 instead of 3.3. The Rosetta demos are meant to work with 3.3.

Most of the rest of the problems you mention are due to the documentation being ancient. As Phil said, apparently what you want to do isn’t officially supported in 3.3, so I guess some of it will have to be made up as you go along.

I assume the RosettaCon2011 demo you are talking about is the protein_dna_interface_design one. It is probably more up-to-date than the manual page is. It’s written for design of a known interface, not for a docking problem, however.

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