How to detect entire beta sheet (multiple strands) using STRIDE on a pdb file?
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3.0 years ago
jl_heights ▴ 10

In PDB files, the header lists the beta sheets and then the strands in those sheets. I prefer to detect beta strands with the STRIDE algorithm instead of with DSSP, which is used for PDB files.

After detecting beta strands, how do I determine which strands are part of the same sheet?

I thought that it might be possible to use hydrogen bonding partners, but PDB files do not contain all hydrogen atoms. Instead I would have to try to detect hydrogen bonds with relaxed constraints on Chimera or generate hydrogen bonds and then probably equilibrate and then detect with more accuracy. How did the PDB header writers do it?

pdb stride dssp protein • 737 views
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