Hello experts,
I used ChemSketch to draw DNA with the presence of probe at the 5' terminal. Later, I convert the Sketch to .sdf and .sdf to .pdb using Discovery Studio. However, when I visualized the output, the DNA looks 'rigid' (picture attached) and the naming & numbering of DNA in pdb file generated from ChemSketch is 'weird' (pdb file attached)..
I'm just wondering is there any other software that can integrate/combine the nucleic acid with chemical structure (probe etc.) as 1 entity (in pdb file format), specifically at 5' or 3' for in silico study?
TQ in advance :)
You could use the 3D-Builder in Maestro (by Schrodinger, also within the free academic version) to generate the DNA and to attach your labeling molecule. The atom names should be correct then.
Discovery Studio and Schrodinger (free visualizar) can be used to creat a double stranded DNA with 3D coordinates from your own sequences. After getting it, you have to minimize it's energy before use any in silico experiments.
Dear Dr Lukas Schulig , Dr Nayim Sepay and Dr Bruno Cramer
Thank you for your informative suggestions.. I will try each of them..
Perhaps I can get my 3D structure and proceed with docking simulation..
Thank you very much once again
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