Question

I am trying to study docking of drug-DNA interaction and for that I need PDB file.

How can I get a pdb file for my custom dsDNA sequence (10-11 base pairs long)?

I will really appreciate if you can please guide me.

Thank you all for your time.

Answer 1

To generate a PDB file for a custom dsDNA sequence, use modeling software to construct the 3D structure and then perform docking using software like FlexX. The RCSB Protein Data Bank provides a repository for existing structures but not custom sequences. Tools like PyMol can be used for visualization.

Step-by-step explanation:

To obtain a PDB file for a custom dsDNA sequence, one option is to use the RCSB Protein Data Bank. Each structure in this database is assigned a unique identification code. For example, the 2GFP code represents the multi-drug resistance efflux pump data set. Although this database is an excellent resource for obtaining existing structures, it does not directly offer custom DNA sequence files. However, to generate a PDB file for a specific DNA sequence, you may use modeling software, like Sybyl, that constructs the 3D structure using known sequences as templates. After constructing your dsDNA, computational docking can be performed. Docking software such as FlexX could be used to study drug-DNA interactions. Afterward, visualization and analysis of the docked conformations are possible with tools like PyMol. It's essential to ensure that the DNA sequence is modeled correctly and that the resulting structure is energetically plausible conforming to established parameters.