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Table 3 Overall descriptor set ranking

From: Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

Type

Final rank (MAD)

Rank ACE

Rank GPCR

Rank NNRTI

Rank PI

ProtFP (Feature) and Z-Scales (3)

4 (±2.0)

8.5

4

7.5

2

Z-Scales (3) and Z-Scales (Avg)

4 (±2.5)

11

1

8.5

4.5

Z-Scales (3)

4.5 (±1.5)

6

5

8.5

2.5

MS-WHIM

5.5 (±2.5)

4

8.5

7

4

Z-Scales (5)

6.5 (±3.5)

3

12.5

11.5

4.5

ProtFP (PCA3)

7 (±2.0)

10

9

5

7.5

Z-Scales (Binned)

7.5 (±2.5)

1.5

6.5

10

7.5

ProtFP (PCA5)

9 (±2.0)

15

5.5

5

9.5

FASGAI

9.5 (±2.5)

6.5

9.5

11

9.5

ProtFP (PCA3) and Z-Scales (Binned)

10 (±3.0)

1.5

8

11

12.5

T_Scales

10 (±2.0)

8.5

13

9

9

VHSE

10 (4.0)

5.5

9

10.5

10.5

BLOSUM

11.5 (±4.5)

13.5

8

10

7.5

ProtFP (PCA8)

12 (±2.0)

13.5

8

10.5

13.5

ST_Scales

13 (±1.0)

12

13.5

13

14.5

ProtFP (Feature)

16 (±0.0)

16

16

1

16

  1. The descriptor sets are sorted based on their median (final) rank calculated over all 14 benchmarks and the MAD associated with this value. Also shown is the rank each descriptor set receives in each individual data set (calculated over the four benchmarks per data set). The best performance is achieved by combining the Z-scales (3) with complementary descriptor types (ProtFP (Feature) or Z-scales (Avg)), closely followed by Z-Scales (3), MS-WHIM, and Z-Scales (5).