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Table 2 Results Comparison of 14 Conservation Measures and SMERFS. ROC0.1 scores for 14 conservation measures taken from [6], SMERFS ,and a random control. Results shown are for a blind testing set of Pfam families, employing optimised parameters derived from prior cross-validation. Each score was normalised to a 0–1 range for an alignment, and inverted when necessary so that 1 = max conserved. This score is shown in the table as 'Standard'. Results of an additional, 'optimised' form are also shown, smoothed over a window of W positions, and processed to remove column results with gap content above C g . The score difference column contains optimised – standard ROC0.1 scores.

From: The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction

Interaction Type

Conservation Measure

Reference

ROC0.1 score (standard)

Parameters

ROC0.1 score (optimised)

Score Difference

    

W

C g

  

Domain

Williamson

[28]

0.0087

3

1

0.0098

0.0011

 

Kabat

[29]

0.0079

5

1

0.0088

0.0009

 

Karlin

[31]

0.0074

7

1

0.0086

0.0012

 

Sander

[36]

0.0078

3

1

0.0083

0.0005

 

Valdar

[32]

0.0075

7

1

0.0081

0.0006

 

Taylor

[33]

0.0070

9

1

0.0080

0.0010

 

Zvelebil

[52]

0.0070

9

1

0.0079

0.0009

 

SMERFS

 

0.0056

9

1

0.0071

0.0015

 

Armon

[14]

0.0063

9

0.8

0.0067

0.0004

 

Jores

[30]

0.0050

9

0.9

0.0064

0.0014

 

Schneider

[36]

0.0049

5

0.6

0.0062

0.0013

 

Gerstein

[35]

0.0049

5

0.6

0.0062

0.0013

 

Thompson

[26]

0.0060

7

1

0.0062

0.0002

 

Mirny

[34]

0.0059

9

0.7

0.0057

-0.0002

 

Randomscore

 

0.0048

7

1

0.0052

0.0004

 

Lancet

[27]

0.0008

1

0.3

0.0051

0.0043

Small Molecule

Williamson

[28]

0.0114

5

1

0.0122

0.0008

 

Kabat

[29]

0.0128

3

1

0.0120

-0.0008

 

Valdar

[32]

0.0120

1

1

0.0120

0.0000

 

Taylor

[33]

0.0113

1

1

0.0113

0.0000

 

Karlin

[31]

0.0121

9

1

0.0110

-0.0011

 

Thompson

[26]

0.0073

1

0.9

0.0108

0.0035

 

Zvelebil

[52]

0.0110

9

1

0.0108

-0.0002

 

Armon

[14]

0.0107

1

1

0.0107

0.0000

 

Schneider

[36]

0.0091

1

0.8

0.0102

0.0011

 

Gerstein

[35]

0.0091

1

0.8

0.0102

0.0011

 

Lancet

[27]

0.0014

1

0.2

0.0097

0.0083

 

Sander

[36]

0.0091

3

1

0.0093

0.0002

 

Jores

[30]

0.0090

9

0.8

0.0090

0.0000

 

SMERFS

 

0.0057

9

1

0.0079

0.0022

 

Mirny

[34]

0.0089

9

0.6

0.0078

-0.0011

 

Randomscore

 

0.0049

7

1

0.0053

0.0004

Combined

Williamson

[28]

0.0107

5

1

0.0112

0.0005

 

Kabat

[29]

0.0106

3

1

0.0108

0.0002

 

Karlin

[31]

0.0099

7

1

0.0108

0.0009

 

Valdar

[32]

0.0100

7

1

0.0102

0.0002

 

Taylor

[33]

0.0093

9

1

0.0098

0.0005

 

Zvelebil

[52]

0.0091

9

1

0.0097

0.0006

 

Sander

[36]

0.0091

3

1

0.0096

0.0005

 

Schneider

[36]

0.0064

5

0.5

0.0078

0.0014

 

Gerstein

[35]

0.0064

5

0.5

0.0078

0.0014

 

SMERFS

 

0.0057

9

1

0.0077

0.0020

 

Armon

[14]

0.0083

9

0.8

0.0076

-0.0007

 

Jores

[30]

0.0066

9

0.9

0.0074

0.0008

 

Lancet

[27]

0.0009

1

0.2

0.0073

0.0064

 

Thompson

[26]

0.0065

9

1

0.0068

0.0003

 

Mirny

[34]

0.0074

9

0.7

0.0067

-0.0007

 

Randomscore

 

0.0049

7

1

0.0053

0.0004