I have run peptide-DNA (single stranded) complex simulation. I understand that the helical structure of ssDNA can not be intact during simulation. But, I wonder how to determine the most feasible folding of ssDNA from MDS analysis. The image of complex structure is attached. I would be grateful for your answer.
You would normally built up a conformational energy landscape e.g. using PCA. See references here: https://www.researchgate.net/publication/326147685_Replica_Based_Protein_Structure_Sampling_Methods_Compromising_between_Explicit_and_Implicit_Solvent
You can also try things like RMSD cluster analysis.
Generally, you can't. MD simulation is not that powerful. If you're asking what's the most populated folding *in your simulation*, clustering analysis is the way to go.
https://ctlee.github.io/BioChemCoRe-2018/clustering/
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