Like in haddock aptamer-protein docking case, we need pdb file of ssDNA. I have used m fold for prediction of secondary structure of ssDNA but it does not provide any pdb file of the same.
you can create ssDNA of required sequence using make-na server
http://structure.usc.edu/make-na/server.html
Dear Mandar Kulkarni,
In this server, they ask for helix type like A or B. But i do not want to give any helix type because ssDNA would fold into some shape on its own according to its sequence. Can you suggest me some other software or server?
Dear Tanu Bhardwaj,
Actually, standard geometries of ssDNA structures are modelled according particular set of structural parameters in modelling software such as NAB or make-na web-server. So, most likely you will get extended ssDNA (B-form /A-form) from any such methods. The possible solution, I am aware , is running simulation on such ssDNA and get various configurations possible.
Unfortunately, I am not aware of any other method that will helpful to you. Hope this helps.
Dear Mandar Kulkarni,
Thank you for your suggestion. I have used m fold for getting various configurations of a particular sequence of ssDNA. But i do not get pdb file for those configurations.
I have never used mfold. but if your output contain XYZ coordinates configurations, then you can try, openbabel to convert xyz to pdb.
Dear Jun Li,
I do not know why this software does not work with windows.
Tanu, X3DNA works in Windows OS. i run it using Cygwin (and Mintty terminal). The program is written in Ruby so you need to have ruby installed in Cygwin: try "ruby -v" in Mintty terminal to see if, and which version of, Ruby is installed.
I have made attempts to use some of the above mention links and still not successful in my attempst to create a PDB structure of ssDNA
Martin Klvana I tried using X3DNA and it works but without hydrogens. Would it be possible to generate a PDB structure of ssDNA with hydrogens? Thanks.
Emilie Cauët , not with X3DNA, as far as i know; i add the hydrogens using Qprep program, which is included in Q molecular dynamics simulation package.
Martin Klvana I generated a pdb file using X3DNA but when I try to read it using Qprep6 (readpdb "filename.pdb"), I got the following error messages: "ERROR: Residue number 1 is of unknown type DT" (same for each residue). Should I do an extra step ? Many thanks.
Emilie Cauët , yes, prior to the readpdb command, read the library in which the nucleotides are defined: readlib
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