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Table 1 Default parameter values

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

  1. For each kernel function a couple of values are provided for \(\eta\) (the proportionality constant of the bandwidth parameters) that indicate the values for kernel k-means (KK) and spectral clustering (SP), respectively