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Table 2 Top 25 performing SeqFEATURE models

From: The SeqFEATURE library of 3D functional site models: comparison to existing methods and applications to protein function annotation

Model name

AUC

Z-cutoff-100

Sens-100

Z-cutoff-99

Sens-99

Z-cutoff-95

Sens-95

No. of examples

ADH_ZINC.2.HIS.ND1

1.0000

3.4172

1.0000

2.4184

1.0000

1.7128

1.0000

6

CARBOXYLESTERASE_B_1.11.SER.OG

1.0000

5.2823

1.0000

2.5415

1.0000

1.7047

1.0000

6

GLYCOSYL_HYDROL_F5.7.GLU.OE1

1.0000

3.8385

1.0000

2.7188

1.0000

1.8787

1.0000

6

HIPIP.7.CYS.SG

1.0000

4.8473

1.0000

2.7401

1.0000

1.7795

1.0000

5

RNASE_T2_1.4.HIS.NE2

1.0000

4.0910

1.0000

2.6209

1.0000

1.6521

1.0000

5

THIOL_PROTEASE_ASN.6.ASN.ND2

1.0000

3.8379

1.0000

2.5982

1.0000

1.8237

1.0000

5

THIOL_PROTEASE_ASN.6.ASN.OD1

1.0000

4.1252

1.0000

2.6255

1.0000

1.7985

1.0000

5

TYR_PHOSPHATASE_1.3.CYS.SG

1.0000

5.4246

1.0000

2.7473

1.0000

1.7596

1.0000

8

CYTOCHROME_P450.8.CYS.SG

1.0000

4.1254

0.8333

2.4019

1.0000

1.7526

1.0000

12

PEROXIDASE_2.8.HIS.ND1

0.9999

3.6628

0.8000

2.6225

1.0000

1.7515

1.0000

5

BPTI_KUNITZ_1.8.CYS.SG

0.9999

3.5059

0.8333

2.2843

1.0000

1.7820

1.0000

6

4FE4S_FERREDOXIN.5.CYS.SG

0.9999

2.7500

0.4000

1.5623

1.0000

1.2660

1.0000

17

ADH_SHORT.3.TYR.OH

0.9999

5.0745

0.1176

2.2891

1.0000

1.6249

1.0000

20

TRYPSIN_SER.6.SER.OG

0.9998

5.4646

0.0000

2.1696

1.0000

1.6085

1.0000

17

GLYCOSYL_HYDROL_F5.7.GLU.OE2

0.9998

3.9203

0.8333

2.6280

1.0000

1.8757

1.0000

6

4FE4S_FERREDOXIN.1.CYS.SG

0.9998

3.1084

0.1000

2.0501

1.0000

1.5589

1.0000

20

PEROXIDASE_2.8.HIS.NE2

0.9997

3.9233

0.6000

2.5753

1.0000

1.8144

1.0000

5

BETA_LACTAMASE_B_1.6.HIS.ND1

0.9997

5.3466

0.8000

2.7205

1.0000

1.7821

1.0000

5

ADH_ZINC.2.HIS.NE2

0.9996

3.8970

0.6667

2.4840

1.0000

1.7499

1.0000

6

LIPASE_SER.7.SER.OG

0.9995

4.7293

0.6250

2.5387

1.0000

1.7350

1.0000

8

ASP_PROTEASE.4.ASP.OD2

0.9994

3.7837

0.4706

2.2973

1.0000

1.7238

1.0000

17

IMP_1.4.ASP.OD2

0.9994

3.9608

0.6000

2.5508

1.0000

1.8129

1.0000

5

BETA_LACTAMASE_B_1.4.HIS.ND1

0.9993

3.8683

0.8000

2.6032

1.0000

1.8239

1.0000

5

BETA_LACTAMASE_B_1.8.ASP.OD1

0.9991

4.6363

0.6000

2.9202

1.0000

1.8558

1.0000

5

4FE4S_FERREDOXIN.3.CYS.SG

0.9991

3.4191

0.0000

2.0044

0.9500

1.4919

1.0000

20

  1. For each model, we report (from left to right) the AUC, the Z-score for which all negatives are correctly predicted, the sensitivity (Sens) at this Z-score, the Z-score for which 99% of negatives are correctly predicted, the associated sensitivity, and the Z-score and associated sensitivity for 95%. The final column reports the number of positive examples of the one-dimensional motif found in the ASTRAL40 compendium of the PDB.
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Genome Biology

ISSN: 1474-760X

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