Structural Analysis using 3-D structure of Protein rather than SSE (alignment)

[Former user]

Hello everyone, I was just wondering if there is a way to compare protein structures by the 3-D structure rather than comparing the secondary structure elements.

[Xinqiu Yao]

Hi,

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Can you tell more detail about your question? There are multiple ways to compare structures, RMSD (root mean square deviation), for example. Is this what you ask?

[Daniel Lim]

I guess I wanted to ask if there was any way to compare a structure based off its normal mode analysis or the flow of the protein itself? I have a PDB file right now that I also have to minimize and I am not sure how I can minimize it, so I can run the NMA afterwards.