Question

I have two .pdb files with two ssDNAs, which should form some specific shape when closed together. Is it possible to model/simulate this merging somehow?

Answer 1

Yes, it is possible to model and simulate the merging of two ssDNAs represented by .pdb files using molecular dynamics simulations.

Step-by-step explanation:

It is possible to model and simulate the merging of two ssDNAs represented by .pdb files. One way to do this is through molecular dynamics simulations, which use methods of physics and computer algorithms to simulate the movement and interactions of atoms and molecules over time. By setting up the initial structure of the ssDNAs in a simulation software and applying appropriate force fields, you can observe how the ssDNAs come together and form a specific shape. These simulations provide insights into the conformational changes and stability of DNA structures.