From: Assignment of structural domains in proteins using diffusion kernels on graphs
Parameter | Default value | Description |
---|---|---|
\({\eta }_{{LED}}\) | \(6 \times 10^{-3}\) (KK), \(4 \times 10^{-3}\) (SP) | The bandwidth coefficient of the LED kernel |
\({\eta }_{{MD}}\) | \(2.5 \times 10^{-1}\) (KK), \(8 \times 10^{-1}\) (SP) | The bandwidth coefficient of the MD kernel |
\({\eta }_{{MED}}\) | \(4 \times 10^{-1}\) (KK), \(3.5 \times 10^{-1}\) (SP) | The bandwidth coefficient of the MED kernel |
\({\eta }_{{RL}}\) | \(2.1 \times 10^{-2}\) (KK), \(2.2 \times 10^{-2}\) (SP) | The bandwidth coefficient of the RL kernel |
MDS | 27 | The minimum domain size |
MHS | 30 | The maximum alpha-helix size to merge |
MSS | 27 | The minimum segment size |
SDR | 1.5 | The maximum segment to domain count ratio |