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Help me in understanding the PDB file

Can anybody please explain the below line to me. "We took the structure and coordinates of nogalamycin from the X-ray structure determined in PDB code = 1D17" What do I need to download from there.... …
dnalectronics's user avatar
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Drug-DNA complex simulation using AMBER

I want to carry out the simulation of drug-dna complex by placing the drug molecule at particular site in my DNA sequence (intercalating site). I have PDB files of both drug and DNA sequence. I will t …
dnalectronics's user avatar
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Generating intercalation site in DNA for custom sequence

Thank you for your help. Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or vi …
dnalectronics's user avatar