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?
There are various ways that you could do this.
- CATH is a hierarchical classification system
- SCOP is another such system with a different hierarchy
- PTGL is the protein topology graph library
- 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.