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normal assigning secondary structure

  • jeremyeadler
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12 years 10 months ago #693 by jeremyeadler
assigning secondary structure was created by jeremyeadler
Hi

I have a protein whose secondary structure is all coil,turn, and bend according to dssp. Would all of these fall under "coil" as far as secondary structure assignment via seq2itp goes? Would it be wiser to use an elastic network?

thanks

Jeremy

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12 years 10 months ago #697 by xavier
Replied by xavier on topic assigning secondary structure

jeremyeadler wrote: Hi

I have a protein whose secondary structure is all coil,turn, and bend according to dssp. Would all of these fall under "coil" as far as secondary structure assignment via seq2itp goes? Would it be wiser to use an elastic network?

thanks

Jeremy


If you define all the protein into coil it won't have any given secondary structure ... so it depends the system you are looking at!

An elastic network would be useful only if the protein has a given structure as the EN would only allow it to fluctuate around a defined conformation.

XAvier.

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  1. Force Fields
  3. Proteins
  5. assigning secondary structure
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