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Suppose I have number of PDB files of proteins. How can I get the number of folds present in these proteins? Is the fold count derivable from the PDB files? If so, how?

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closed as too broad by MattDMo, AliceD, kmm, James, rg255 Sep 28 '16 at 10:06

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  • $\begingroup$ How do you calculate a fold? Amino acid residues in a protein in vivo always have some angle between them - the carbon backbone is never in a straight line. I'm afraid this question is far too broad. $\endgroup$ – MattDMo Sep 22 '16 at 14:02
  • $\begingroup$ Do you mean 'fold' as in the topology? So alpha-beta-barrel, sandwich, key-barrel, etc? $\endgroup$ – gilleain Sep 22 '16 at 14:05
  • $\begingroup$ @gilleain yes exactly... $\endgroup$ – girl101 Sep 22 '16 at 14:56
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There are various ways that you could do this.

  1. CATH is a hierarchical classification system
  2. SCOP is another such system with a different hierarchy
  3. PTGL is the protein topology graph library
  4. Tops motif will scan PDB files and match patterns against it

How you actually apply these tools or lookup within these systems is documented on their websites. However, it depends on what you want to do - look up published structures, or new experimental data.

I should point out that writing software from scratch to determine the fold of a protein may be tricky.

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  • $\begingroup$ this is what i wanted to know... writing from scratch would be difficult.... $\endgroup$ – girl101 Sep 22 '16 at 15:28

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