Please suggest me some DNA structure modeling tools or server or software where I can generate DNA structure by giving known DNA sequence and generate a structural coordinate file to use it DNA-protein interaction study.
Please have a look at this question (and its answers): https://www.researchgate.net/post/How_to_convert_an_amino_acid_sequence_into_readable_PDB_file_by_chimera_or_pymol_software
It i far from being an easy task and there is no easy use tool to verify the result of the work in the end.
You might try 3D-DART: a DNA structure modelling server: http://haddock.chem.uu.nl/dna/dna.php , described in https://academic.oup.com/nar/article/37/suppl_2/W235/1126836
The server provides an easy interface to a powerful collection of tools for the generation of DNA-structural models in custom conformations.
You can use UCSF Chimera tool to build helical DNA.
Open Chimera --> Tool --> Structure Editing --> Build Structure --> helical DNA/RNA --> Past DNA sequence --> Apply
Link : https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecontrib.html
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