Supplementary Table 3.  List of the 92 protein sequences used to test the SVM classifier for DNA-

 binding residues.

PDB ID chain

Structure resolution (Å)

Sequence annotation

1A0A_A

2.80

Yeast phosphate system positive regulatory protein Pho4 (bHLH)

1AM9_A

2.30

Human sterol regulatory element binding protein 1A

1AN4_A

2.90

Human USF protein bHLH domain

1C9B_A

2.65

Human general transcription factor IIB

1CEZ_A

2.40

Bacteriophage T7 RNA polymerase

1CF7_B

2.60

Human transcription factor Dp-2

1CW0_A

2.30

E. coli DNA mismatch endonuclease

1D0E_A

3.00

Moloney murine leukemia virus reverse transcriptase

1D5Y_A

2.70

E. coli Rob transcription factor

1DCT_A

2.80

DNA (cytosine-5) methylase HaeIII from Haemophilus aegyptius

1DFM_A

1.50

Endonuclease Bglii from Bacillus subtilis

1DH3_A

3.00

Transcription factor CREB from Mus musculus

1EA4_A

2.95

Transcriptional repressor copG from Streptococcus agalactiae

1EBM_A

2.10

Human 8-oxoguanine glycosylase

1EMH_A

1.80

Human uracil-DNA glycosylase

1EOO_A

2.16

E. coli type II restriction enzyme EcoRV

1F2I_G

2.35

Zinc finger protein from Mus musculus

1F4K_A

2.50

Replication termination protein from Bacillus subtilis

1F6O_A

2.40

Human 3-methyl-adenine DNA glycosylase

1FIU_A

1.60

Type II restriction enzyme Ngomiv from Neisseria gonorrhoeae

1FJX_A

2.26

DNA methyltransferase Hhai from Haemophilus haemolyticus

1FLO_A

2.65

Yeast recombinase Flp

1FZP_B

2.95

Staphylococcal accessory regulator A from Staphylococcus aureus

1GD2_E

2.00

Yeast transcription factor Pap1

1GXP_A

2.50

E. coli phosphate regulon transcriptional regulatory protein

1H88_A

2.80

Human CCAAT enhancer binding protein beta

1H9D_A

2.60

Human Core Binding Factor (CBF) alpha subunit

1HLV_A

2.50

Human major centromere autoantigen B

1I3J_A

2.20

Intron-associated endonuclease 1

1IAW_A

2.40

Type II restriction enzyme Naei from Nocardia aerocolonigenes

1IC8_A

2.60

Human hepatocyte nuclear factor 1-alpha

1J1V_A

2.10

E. coli chromosomal replication initiator protein dnaA

1JE8_A

2.12

E. coli nitrate/nitrite response regulator protein Nar1

1JEY_A

2.50

Human ATP-dependent DNA helicase II 70 kDa subunit (Ku70)

1JEY_B

2.50

Human ATP-dependent DNA helicase II 80 kDa subunit (Ku80)

1JFI_A

2.62

Human transcription regulator Nc2 alpha chain

1JFI_B

2.62

Human transcription regulator Nc2 beta chain

1JJ4_A

2.40

Human papillomavirus type 18 regulatory protein E2

1JT0_A

2.90

Transcriptional regulator Qacr repressor from Staphylococcus aureus

1K79_D

2.40

C-Ets-1 protein from Mus musculus

1K82_A

2.10

E. coli formamidopyrimidine-DNA glycosylase

1KU7_A

2.40

RNA polymerase sigma subunit from Thermus aquatics

1KX5_A

1.94

Histone H3 from Xenopus laevis

1KX5_B

1.94

Histone H4 from Xenopus laevis

1KX5_C

1.94

Histone H2A from Xenopus laevis

1KX5_D

1.94

Histone H2B from Xenopus laevis

1L3L_A

1.66

Transcriptional activator traR from Agrobacterium tumefaciens

1LB2_B

3.10

E. coli DNA-directed RNA polymerase alpha chain

1LPQ_A

3.14

Human DNA topoisomerase I

1LQ1_A

2.30

Transcription factor Spo0A from Bacillus subtilis

1LRR_A

2.65

E. coli Seqa replication inhibitor

1LV5_A

1.95

DNA polymerase I from Bacillus stearothermophilus

1M5R_A

1.80

Bacteriophage T4 DNA beta-glucosyltransferase

1MM8_A

2.80

E. coli Tn5 transposase

1MNN_A

1.40

Yeast sporulation specific transcription factor Ndt80

1N6J_A

2.20

Human myocyte-specific enhancer factor 2B

1NLW_A

2.00

Human Max protein bHLH domain

1NVP_C

2.10

Human transcription initiation factor IIA beta (TFIIA P35)

1ODH_A

2.85

Transcription factor GCM1 from Mus musculus

1OSB_A

2.65

E. coli Conjugative relaxase Trwc protein

1P7D_A

2.95

Bacteriophage lambda integrase

1PP8_F

3.05

39 Kda initiator binding protein from Trichomonas vaginalis

1PT3_A

2.50

E. coli nuclease Colicin E7

1PUF_B

1.90

Human pre-B-cell leukemia transcription factor-1

1PVR_A

2.65

Recombinase Cre from bacteriophage p1

1Q9X_A

2.69

Bacteriophage rb69 DNA polymerase

1QRV_A

2.20

Drosophila high mobility group protein D (HMG-D)

1QSS_A

2.30

DNA polymerase I from Thermus aquaticus

1R71_A

2.20

E. coli transcriptional repressor protein Korb

1R7M_A

2.25

Yeast intron-encoded endonuclease I-Scei

1R8D_A

2.70

Transcription activator Mtan from Bacillus subtilis

1RH6_A

1.70

Bacteriophage lambda excisionase

1S9F_A

2.00

DNA polymerase IV from Sulfolobus solfataricus

1SA3_A

1.95

Type II restriction enzyme Mspi from Moraxella sp

1SFU_A

2.00

34L protein (DNA-binding) from Yaba-like disease virus

1SKN_P

2.50

Transcription factor Skn-1 from Caenorhabditis elegans

1T2K_A

3.00

Human interferon regulatory factor 3

1T2K_D

3.00

Human cyclic-AMP-dependent transcription factor Atf-2

1T3N_A

2.30

Human DNA polymerase I

1T8E_A

2.54

Bacteriophage T7 DNA polymerase

1T8E_B

2.54

E. coli thioredoxin 1 in the T7 DNA polymerase ternary complex

1T9I_A

1.60

DNA endonuclease I-Crei from Chlamydomonas reinhardtii

1TTU_A

2.85

C. elegans Lin-12/Glp-1 transcriptional regulator

1TX3_A

2.50

Type II restriction enzyme HindII from Haemophilus influenzae

1U3E_M

2.92

Bacteriophage sp01 homing endonuclease Hnh

1VAS_A

2.75

Coliphage T4 endonuclease V

1X9N_A

3.00

Human DNA ligase I

1XPX_A

2.80

Drosophila Prospero protein (homeodomain)

1YFJ_A

2.69

Bacteriophage T4 DNA adenine methylase

1Z63_A

3.00

Helicase of the Snf2/Rad54 family from Sulfolobus solfataricus

2DNJ_A

2.00

Deoxyribonuclease I (Dnase I) from Bos taurus

3ORC_A

3.00

Bacteriophage lambda Cro repressor