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 |