Table 3 Decomposition methods.
From: Towards accurate modeling of noncovalent interactions for protein rigidity analysis
Decomposition Method | Description |
|---|---|
1 | All-floppy decomposition |
2 | All-rigid decomposition |
3 | KINARI v1.0, default options |
4 | KINARI, vary hydrogen bond energy cutoff and exclude weak hydrogen bonds |
5 | KINARI, vary hydrogen bond energy cutoff and model weak hydrogen bonds as bars |
6 | KINARI, use default options for hydrogen bonds. compute hydrophobics and assign energy with LJ-potential. Exclude weak hphobes and model the rest as bars |
7 | KINARI, same as Method 6, but vary the hydrogen bond energy cutoff and model the weaker hydrogen bonds as bars |