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Table 5 The comparison of the performance of the four clustering algorithms over different matrix transformation methods by various indices (Dunn, Davies–Bouldin, eta-squared and omega-squared) and correlations between MSt and MSb of clusters

From: The comparison of automated clustering algorithms for resampling representative conformer ensembles with RMSD matrix

Transformation methods

Clustering algo.

Dunn mean (SD)

Davies-Bouldin mean (SD)

Eta-squared mean (SD)

Omega-squared mean (SD)

Cor (MSt, MSb)

Lower triangle

RCKmeans

0.2 (0.24)

8.06 (4.55)

0.32 (0.18)

0.28 (0.16)

0.82

RCDTC

0.23 (0.24)

6.73 (3.63)

0.4 (0.14)

0.35 (0.14)

0.9

RCPCA

0.18 (0.15)

7.22 (4.53)

0.45 (0.09)

0.33 (0.12)

0.83

RCPCA_RBF

0.14 (0.12)

8.84 (5.33)

0.32 (0.11)

0.26 (0.12)

0.78

Upper triangle

RCKmeans

0.17 (0.29)

8.06 (4.55)

0.32 (0.18)

0.27 (0.17)

0.82

RCDTC

0.21 (0.24)

6.58 (3.2)

0.39 (0.14)

0.34 (0.15)

0.89

RCPCA

0.18 (0.18)

7.02 (3.46)

0.45 (0.08)

0.34 (0.11)

0.82

RCPCA_RBF

0.14 (0.14)

8.66 (5.02)

0.33 (0.1)

0.26 (0.11)

0.78

Average

RCKmeans

0.2 (0.22)

8.31 (5.32)

0.34 (0.18)

0.29 (0.16)

0.82

RCDTC

0.23 (0.24)

6.61 (3.26)

0.41 (0.14)

0.35 (0.15)

0.87

RCPCA

0.17 (0.13)

7.24 (4.02)

0.44 (0.09)

0.33 (0.12)

0.81

RCPCA_RBF

0.14 (0.12)

8.54 (4.64)

0.33 (0.11)

0.27 (0.11)

0.78

Reciprocal

RCKmeans

0.21 (0.24)

7.5 (3.57)

0.33 (0.18)

0.29 (0.17)

0.82

RCDTC

0.22 (0.24)

6.8 (3.51)

0.4 (0.14)

0.35 (0.15)

0.91

RCPCA

0.17 (0.13)

6.83 (3.8)

0.45 (0.08)

0.34 (0.11)

0.82

RCPCA_RBF

0.14 (0.11)

8.74 (5.07)

0.32 (0.11)

0.26 (0.11)

0.79

Non-reciprocal

RCKmeans

0.2 (0.22)

7.8 (4.05)

0.33 (0.17)

0.29 (0.16)

0.81

RCDTC

0.23 (0.24)

6.68 (3.29)

0.4 (0.14)

0.35 (0.15)

0.91

RCPCA

0.19 (0.15)

6.87 (3.57)

0.46 (0.07)

0.35 (0.11)

0.81

RCPCA_RBF

0.14 (0.12)

8.96 (5.22)

0.32 (0.11)

0.26 (0.12)

0.78