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PDB ID Mentions in PubMed Central Article count: 17

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PDB ID Mentions in PubMed Central

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Predicting specificity-determining residues in two large eukaryotic transcription factor families.

(2005) Nucleic Acids Res 33

PubMed: 16085755 | PubMedCentral: PMC1183107 | DOI: 10.1093/nar/gki755

Figure 5 Crystal structure of GCN4 bound to DNA (pdb:1YSA) ( 62 ).

Publication Year: 2005

Protein-DNA binding specificity predictions with structural models.

(2005) Nucleic Acids Res 33

PubMed: 16246914 | PubMedCentral: PMC1270944 | DOI: 10.1093/nar/gki875

Table 2 Experimental binding site and weight matrix dataset Name PDB code Method (Res., Å) N seq Organism Reference λR 1lmb X-ray (1.8) – a λ-Phage ( 51 ) CroR 6cro X-r... y (3.0) – a λ-Phage ( 52 ) AtERF1 1gcc NMR (NA) – a A.thaliana ( 45 ) c-Myb 1mse NMR (NA) – a M.musculus ( 47 ) Zif268 1aay X-ray (1.6) 6 b M.musculus ( 31 ) Ndt80 1mnn X-ray (1.4) 8 b S.cerevisiae ( 34 ) Gcn4p 1ysa X-ray (2.9) 9 c S.cerevisiae ( 35 , 36 ) MAT a 1/α2 1yrn X-ray (2.5) 19 c S.cerevisiae ( 30 ) EcR/Usp 1r0o X-ray (2.24) 33 c Drosophila melanogaster ( 57 ) Ttk 2drp X-ray (2.8) 16 c D.melanogaster – Prd(homeo) 1fjl X-ray (2.0) 15 c D.melanogaster ( 37 ) Ubx/Exd 1b8i X-ray (2.4) 4 b D.melanogaster – Trl 1yui NMR (NA) 5 c D.melanogaster – MetJ 1mj2 X-ray (2.4) 16 c E.coli ( 32 ) TrpR 1tro X-ray (1.9) 15 c E.coli ( 32 , 33 ) PhoB 1gxp X-ray (2.5) 16 c E.coli ( 32 ) Ihf 1ihf X-ray (2.5) 27 c E.coli ( 32 ) DnaA 1j1v X-ray (2.1) 9 c E.coli ( 32 ) PurR 2puc X-ray (2.7) 23 c E.coli ( 32 ) Crp 1run X-ray (2.7) 50 c E.coli ( 32 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

Table 4 Summary of binding site energy predictions PDB Z PDB 〈 Z site 〉 Rank L 1mnn −3.69 −2.54 14 12 1ysa −3.38 −2.53 1 7 1yrn −4.30 −3.34 – 19 1aay −3.70 −3.60 13 10 1b8i −3.22 −2.74 8 10 1r0o −3.80 −2.88 – 15 2drp −3.77 −2.76 6 11 1yui −2.38 −2.48 91 7 1fjl −3.22 −2.93 4507 13 1gxp −4.17 −3.06 – 20 1ihf −3.41 −1.12 – 34 1j1v −4.20 −3.36 13 13 1mj2 −3.09 −2.13 – 16 1run −3.50 −2.32 – 22 1tro −3.73 −2.57 – 18 2puc −3.88 −3.68 – 16 Z PDB is the Z -score ( Equation 16 ) for the protein–DNA binding energy with the binding site found in the protein–DNA structure; 〈 Z site 〉 is the average Z -score for protein–DNA binding energies with binding sites listed in Table 2 ; Rank is the rank of the binding energy for the structural site in the ensemble of 4 L sequences ( L is the binding site length).

Publication Year: 2005

The signaling helix: a common functional theme in diverse signaling proteins.

(2006) Biol Direct 1

PubMed: 16953892 | PubMedCentral: PMC1592074 | DOI: 10.1186/1745-6150-1-25

To better explore this functional proposal we constructed a model of the S-helix using other parallel CCs as a template (e.g. pdb 1ysa [ 45 ]).

A model of the S-Helix domain was constructed using other parallel CCs as templates (e.g. PDB: 1YSA).

Publication Year: 2006

Energetics of protein-DNA interactions.

(2007) Nucleic Acids Res 35

PubMed: 17259221 | PubMedCentral: PMC1851630 | DOI: 10.1093/nar/gkl1103

The set then contains the following 30 structures: 1aay, 1apl, 1az0, 1azp, 1bc7, 1bhm, 1bp7, 1ca5, 1cdw, 1cma, 1cw0, 1ecr, 1efa, 1glu, 1hcq, 1hcr, 1ihf, 1ipp, 1lmb, 1mdy, 1nfk, 1oct, 1par, 1pue, 1qrv,... 1run, 1tro, 1tsr, 1ysa and 1ytf.

Publication Year: 2007

iPDA: integrated protein disorder analyzer.

(2007) Nucleic Acids Res 35

PubMed: 17553839 | PubMedCentral: PMC1933224 | DOI: 10.1093/nar/gkm353

( B ) One pattern derived by WildSpan identifies nine important residues for DNA binding (PDB structure used: 1YSA).

Publication Year: 2007

Insights into protein-DNA interactions through structure network analysis.

(2008) PLoS Comput Biol 4

PubMed: 18773096 | PubMedCentral: PMC2518215 | DOI: 10.1371/journal.pcbi.1000170

Class 1 Class 2 Class 3 Class 4 Class 5 Class 6 Class 7 P-p clusters only P-S clusters only P-B clusters only P-p and P-S clusters (no P-B clusters) P-S and P-B clusters (no P-p clusters) P-p and P-B ... lusters (no P-S clusters) P-p, P-S, and P-B clusters are present Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping clusters Non-overlapping clusters Overlapping P-p, P-B, and P-S clusters Non-overlapping P-p, P-B, and P-S clusters P-p and P-S clusters overlap but not P-B clusters P-S and P-B clusters overlap but not P-p clusters P-p and P-B clusters overlap but not P-S clusters P-P, P-B and P-S clusters occur separately β-Hairpin β-Hairpin Zinc coordinating group Enzymes β-Hairpin β-Hairpin Other α-helices Others Helix turn helix – β-Hairpin β-Sheet Enzymes β-Hairpin 1cma- a 1azp- 1zaa- 1a31- 1ecr- 1bnz- 1ckt- 1ramA 1apl- 1bdt- 1d3u- 1bss- 1ihf- a Enzymes 1bf4- 1a35- 1xbr- a β-Sheet 1vkx- 1lli- Enzymes 1tgh- 1ipp- β-Sheet 7ice- Enzymes 1bhm- a Enzymes 1c9bB Zipper type Others 1cyq- Enzymes Helix turn helix 1vol- Helix turn helix 2dnj- 1dnk- 1bnk- 1cdw- 1an4- 1a3qA 1dctA 2bdp- 1tc3- Enzymes 3orc- 2rve- 1t7pA 1bpx- Enzymes 1hlo- a 1bf5-* 1rv5- 3ktq- 1a74- a Other α-helices 3bam- 1qss- 10mh- 1nfkA 4skn- Helix turn helix 1ssp- 1skn- Helix turn helix 1qsy- 1clq- Zinc coordinating group 5mht- 1fjl- a 1vas- Zipper type 6pax- 2bpf- 1pvi- a 1a1g- Helix turn helix Zinc coordinating group 3pvi- 1ysa- a Other α-helices 2ktq- 1tau- 1aay-* 1gdt- a 1cit- Helix turn helix 1b3t- a 2ssp- 2pvi- 1d66-* 1ignA a 1fok- Zinc coordinating group 4ktq- Other α-helices 1ubd-* 1rpe- 1hcr- a 1lat- Helix turn helix 1qrv- 1zme- 6cro- 1mnm- a 1akh- Zipper type Zinc coordinating group 1yrn- a 1hddC a 1an2- 2gli- a 3cro- a 1pdn- Zipper type Zinc coordinating group 3hddA 1a02- 1a6y- Other α-helices 1a0a- 1aoi- Zinc coordinating group 1glu- 1tsr- a 2nll- a These protein–DNA complexes are also present in DS3 (see Materials and Methods section).

Publication Year: 2008

Reversible pH-controlled DNA-binding peptide nanotweezers: an in-silico study.

(2008) Int J Nanomedicine 3

PubMed: 19337419 | PubMedCentral: PMC2636583 | DOI: null

Methods Peptide design The X-ray crystallographic structure of the native GCN4 (PDB entry: 1YSA), complexed with AP-1 yeast DNA, was obtained from the Protein Data Bank (see Figure 1a ).

Publication Year: 2008

ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors.

(2009) Nucleic Acids Res 37

PubMed: 19483101 | PubMedCentral: PMC2703882 | DOI: 10.1093/nar/gkp449

Figure 1 (a) shows the prediction output of ProteDNA for the polypeptide sequence of Yeast TF GCN4 in the complex with Protein Data Bank (PDB) ( 9 ) ID 1YSA.

( b ) The tertiary structure of the complex with PDB ID 1YSA.

Figure 1 (b) depicts the output of ProteDNA in the tertiary structure of PDB complex 1YSA.

( a ) The partial prediction output of ProteDNA with the polypeptide sequence of Yeast TF GCN4 in PDB complex 1YSA.

Publication Year: 2009

DNA-binding residues and binding mode prediction with binding-mechanism concerned models.

(2009) BMC Genomics 10 Suppl 3

PubMed: 19958487 | PubMedCentral: PMC2788376 | DOI: 10.1186/1471-2164-10-S3-S23

Table 5 Dataset of 253 TF-DNA complexes for DNA-binding residues prediction 253 TF-DNA Complexes 1A02:F 1A02:J 1A0A:A 1A0A:B 1A6Y:A 1A6Y:B 1AKH:A 1AKH:B 1AM9:A 1AM9:B 1AM9:C 1AM9:D 1AN2:A 1AN4:A 1AN4:... 1APL:C 1APL:D 1AU7:A 1AU7:B 1B01:A 1B01:B 1B72:B 1B8I:B 1BDT:A 1BDT:B 1BDT:C 1BDT:D 1BDV:A 1BDV:B 1BDV:C 1BDV:D 1BY4:A 1BY4:B 1BY4:C 1BY4:D 1C0W:A 1C0W:B 1C0W:C 1C0W:D 1CF7:A 1CF7:B 1CGP:A 1CGP:B 1CMA:A 1CMA:B 1CQT:A 1D5Y:A 1D5Y:B 1D5Y:C 1D5Y:D 1D66:A 1D66:B 1DDN:A 1DDN:B 1DDN:C 1DDN:D 1DSZ:A 1DSZ:B 1DU0:A 1DU0:B 1EA4:A 1EA4:B 1EA4:D 1EA4:E 1EA4:F 1EA4:G 1EA4:H 1EA4:J 1EA4:K 1EA4:L 1F2I:G 1F2I:H 1F2I:I 1F2I:J 1F2I:K 1F2I:L 1F5T:A 1F5T:B 1F5T:C 1F5T:D 1FJL:A 1FJL:B 1FJL:C 1FOS:E 1FOS:F 1FOS:G 1FOS:H 1G2D:C 1G2D:F 1G2F:C 1G2F:F 1GDT:A 1GDT:B 1H88:A 1H88:B 1H89:A 1H89:B 1H8A:A 1H8A:B 1H9T:A 1H9T:B 1HCQ:A 1HCQ:B 1HDD:C 1HDD:D 1HF0:A 1HF0:B 1HJB:A 1HJB:B 1HJB:D 1HJB:E 1HLO:A 1HLO:B 1HW2:A 1HW2:B 1HWT:C 1HWT:D 1HWT:G 1HWT:H 1IO4:A 1IO4:B 1JGG:A 1JGG:B 1JNM:A 1JNM:B 1JT0:A 1JT0:B 1JT0:C 1JT0:D 1JWL:A 1JWL:B 1K61:A 1K61:B 1K61:C 1K61:D 1KB2:A 1KB2:B 1KB4:A 1KB4:B 1KB6:A 1KB6:B 1KU7:A 1L3L:A 1L3L:B 1L3L:C 1L3L:D 1LAT:A 1LAT:B 1LB2:A 1LE8:A 1LE8:B 1LLI:A 1LLI:B 1LLM:C 1LMB:3 1LMB:4 1MDY:A 1MDY:C 1MDY:D 1MEY:C 1MEY:F 1MJM:A 1MJM:B 1MJP:A 1MJP:B 1MNM:C 1MNM:D 1NKP:A 1NKP:B 1NKP:D 1NKP:E 1NLW:A 1NLW:B 1NLW:D 1NLW:E 1P47:A 1P47:B 1PAR:A 1PAR:B 1PAR:C 1PAR:D 1PER:L 1PER:R 1PUF:A 1PUF:B 1PYI:A 1PYI:B 1QP9:A 1QP9:B 1QP9:C 1QP9:D 1R0N:A 1RPE:L 1RPE:R 1TF6:A 1TF6:D 1TRO:A 1TRO:C 1TRO:E 1TRO:G 1TRR:A 1TRR:B 1TRR:D 1TRR:E 1TRR:G 1TRR:H 1TRR:J 1TRR:K 1YRN:A 1YRN:B 1YSA:C 1YSA:D 1ZME:C 1ZME:D 2DRP:A 2DRP:D 2HAP:C 2HAP:D 2HDD:A 2HDD:B 2NLL:A 2NLL:B 2OR1:L 2OR1:R 2PRT:A 2QL2:A 2QL2:B 2QL2:C 2QL2:D 2R5Y:A 2R5Y:B 3BPY:A 3CBB:A 3CBB:B 3CO6:C 3COQ:A 3COQ:B 3D0A:A 3D0A:B 3D0A:C 3D0A:D 3DFX:A 3DFX:B 3DZY:A 3DZY:D 3E00:A 3E00:D 3EXJ:A 3EXJ:B 3EXL:A 3HDD:A 3HDD:B 9ANT:A Defining the DNA-binding residue Previous research used various distance cut-offs from 3.5 Å to 6 Å to define DNA-binding residues between proteins and DNA [ 6 - 10 , 14 , 40 , 42 ].

Publication Year: 2009

CLICK--topology-independent comparison of biomolecular 3D structures.

(2011) Nucleic Acids Res 39

PubMed: 21602266 | PubMedCentral: PMC3125785 | DOI: 10.1093/nar/gkr393

Two DNA double-helical fragments bound to proteins (PDB codes 1YSA and 2AYG) are aligned with one another.

Publication Year: 2011

Predicting target DNA sequences of DNA-binding proteins based on unbound structures.

(2012) PLoS One 7

PubMed: 22312425 | PubMedCentral: PMC3270014 | DOI: 10.1371/journal.pone.0030446

PDB Entry name a Protein Seven proteins used as the queries 6CRO RCRO_LAMBD Regulatory protein cro 1MSE MYB_MOUSE Transcriptional activator Myb 1MNN NDT80_YEAST Meiosis-specific transcription factor N... T80 1YRN MATA1_YEAST Mating-type protein A1 1TRO TRPR_ECOLI Trp operon repressor 1RUN CRP_ECOLI Catabolite gene activator 2O61 b NFKB1_HUMAN Nuclear factor NF-kappa-B p105 subunit 13 complexes used for tuning the parameters of the all-atom model 1AAY EGR1_MOUSE Early growth response protein 1 1B8I c UBX_DROME Homeotic protein ultrabithorax EXD_DROME Homeobox protein extradenticle 2DRP TTKB_DROME Protein tramtrack, beta isoform 1FJL PRD_DROME Segmentation protein paired 1GCC ERF1A_ARATH Ethylene-responsive transcription factor 1A 1GXP PHOB_ECOLI Phosphate regulon transcriptional regulatory protein phoB 1J1V DNAA_ECOLI Chromosomal replication initiator protein dnaA 1LMB RPC1_LAMBD Repressor protein CI 1MJ2 METJ_ECOLI Met repressor 2PUC PURR_ECOLI HTH-type transcriptional repressor purR 1R0O USP_DROME Protein ultraspiracle 1YSA GCN4_YEAST General control protein GCN4 1YUI GAGA_DROME Transcription factor GAGA a UniProt entry name.

Entry name Native a Query b Template c CRP_ECOLI 1RUN 2GZW:A 3E6C:C MATA1_YEAST 1YRN 1MH3:A 2HOS:A MYB_MOUSE 1MSE 1GV2:A 1W0T:A NDT80_YEAST 1MNN 1M6U:A 1HJC:A RCRO_LAMBD 6CRO 2A63:A 3CRO:R TRPR_ECOLI 1TRO 1MI7:R 1YSA:D NFKB1_HUMAN 2O61 1NFI:D 1HJC:A a native complexes of the corresponding proteins.

Publication Year: 2012

Re-visiting protein-centric two-tier classification of existing DNA-protein complexes.

(2012) BMC Bioinformatics 13

PubMed: 22800292 | PubMedCentral: PMC3472317 | DOI: 10.1186/1471-2105-13-165

Table 1 Representatives for previous families 54 existing families (Thornton classification) representatives were selected and were validated using Jack-knifing Group Families Representative(s) HTH &#... 000a0;     Cro & repressor 1LMB   Homeodomain 1FJL, 1HDD, 6PAX   LacI repressor 1WET   Endonuclease Fok1 1FOK   Gamma Delta resolvase 1GDT   Hin recombinase 1HCR   RAP1 family 1IGN   Prd paired domain 1PDN   Tc3 transposase 1TC3   Trp repressor 1TRR   Diptheria tox repressor 1DDN   Transcription factor IIB 1D3U   Interferon regulatory 2IRF   Catabolite gene activator protein 1RUO   Transcription factor 1CF7, 3HTS   Ets domain 1BC8 Zinc Co-ordinating       β-β-α zinc finger 1ZAA   Harmone Nuclear Receptor 2NLL   Loop sheet helix 1TSR   GAL4 type 1ZME Zipper type       Leucine Zipper 1YSA   Helix loop helix 1AN2 Other-α Helix       Pappilomavirus 1 E2 2BOP   Histone 1AOI   EBNA1 nuclear protein 1B3T   Skn-1 transcription factor 1SKN   Cre Recombinase 1CRX   High Mobility Group 1QRV   MADS box 1MNM β-Sheet       TATA box binding 1YTB β-Hairpin/Ribbon       MetJ repressor 1CMA   Tus replication terminator 1ECR   Integration host factor 1IHF   Transcription Factor T-domain 1XBR   Hyperthermophile DNA 1AZP   Arc repressor 1PAR Other       ReI homology 1SVC   Stat protein 1BF5 Enzyme       Methyltransferase 6MHT   Endonuclease PvuII 3PVI   Endonuclease ecorV 1RVA   Endonuclease ecorI 1QPS   Endonuclease BamHI 3BAM   Enonuclease V 1VAS   Dnase I 2DNJ   DNA mismatch endonuclease 1CW0   DNA polymerase β 1BPY   DNA Polymerase I 2BDP   DNA Polymerase T7 1T7P,1CLQ   HIV Reverse Transcriptase 2HMI   Uracil DNA glycosylase 1SSP   3-Methyladenine DNA glycosylase 1BNK   Homing endonuclease 1A73, 1BP7   TopoisomeraseI 1A31 For all the 59 selected representatives, PSI-BLAST profiles were again built against dummy database using the earlier profile creation parameters (as described in Methods).

Publication Year: 2012

Genome-wide analysis of bZIP-encoding genes in maize.

(2012) DNA Res 19

PubMed: 23103471 | PubMedCentral: PMC3514857 | DOI: 10.1093/dnares/dss026

( B ) The superposition structure of bZIP domains of ATF-2 (PDB ID: 1T2K, pink), CREB (PDB ID: 1DH3, green), GCN4 (PDB ID: 1YSA, blue) and HY5 (PDB ID: 2OQQ, yellow).

  2 B) were obtained from PDB accession number 1T2K ( Homo sapiens , pink), 1DH3 ( Mus musculus , green), 1YSA ( S. cerevisiae , blue) and 2OQQ ( A. thaliana , yellow), which were the most hits of ZmbZIP proteins by homologous modelling.

Further, the homology modelling was performed and the results show four models to be the best hits to our proteins, including PDB accession number 1T2K ( H. sapiens ), 1DH3 ( M. musculus ), 1YSA ( S. cerevisiae ) and 2OQQ ( A. thaliana ).

Publication Year: 2012

Protein-DNA docking with a coarse-grained force field.

(2012) BMC Bioinformatics 13

PubMed: 22966980 | PubMedCentral: PMC3522568 | DOI: 10.1186/1471-2105-13-228

Table 1 Crystallographic protein-DNA complexes (designated by PDB id) with matching experimental binding free energies extracted from ProNIT database PDB Chains ΔG /kcal mol −1 1AAY A/... C −11.5 [ 26 ] 1AZ0 AB/CD −17.4 [ 27 ] 1B72 AB/DE −9.0 [ 28 ] 1BHM AB/CD −11.7 [ 29 ] 1CEZ A/TN −10.8 [ 30 ] 1CMA AB/CD −5.4 [ 31 ] 1D02 AB/CD −8.1 [ 32 ] 1ECR A/BC −15.6 [ 33 ] 1IHF AB/CD −10.3 [ 34 , 35 ] 1PUE E/AB −9.7 [ 36 ] 1QRV A/CD −7.4 [ 37 , 38 ] 1YSA CD/AB −9.5 [ 39 ] 1PUF A/DE −9.2 [ 28 ] 1TRO AC/IJ −12.6 [ 40 - 42 ] 1UBD C/AB −8.5 [ 43 ] A set including crystallographic structures of protein-DNA complexes with corresponding binding affinities provided by Zhang et al. [ 44 ] was considered as an alternative source of data.

Publication Year: 2012

Aureochrome 1 illuminated: structural changes of a transcription factor probed by molecular spectroscopy.

(2014) PLoS One 9

PubMed: 25058114 | PubMedCentral: PMC4110000 | DOI: 10.1371/journal.pone.0103307

Aureochrome 1 shares high homology with the general control protein (GCN4) from S. cerevisiae (PDB entry: 1YSA [14] ) not only in its primary sequence ( Fig. 7 ) but also in the sequences of the respe... tive target DNA which is ATGACTCAT for GCN4 and TGACGT for aureochrome 1, respectively.

The structure was modeled on the basis of the GCN4 crystal structure (PDB:1YSA [14] ).

Publication Year: 2014

PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4482085

In the available DNA–protein co-crystal structures of the yeast TF GCN4 (PDB ID: 1YSA) ( 58 ), the hydrogen bonds binding to the 5′-phosphate groups of the plus and minus motifs are do... ated by amino acid residues (Thr236, Arg240, Arg-241, Arg245 and Lys246) from the left and right monomers.

Publication Year: 2015

Quantitative evaluation of protein-DNA interactions using an optimized knowledge-based potential.

(2005) Nucleic Acids Res 33

PubMed: 15673715 | PubMedCentral: PMC548349 | DOI: 10.1093/nar/gki204

Non-TF/DNA refers to 27 non-transcription factor/DNA complexes (including 1mse, 1tro, 1ca5, 2ezd, 1lcc, 1cjg, 1gcc, 1azp, 1az0, 1b69, 1tf3, 1bhm, 1ecr, 1cw0, 1hcr, 1yui, 1sx9, 7icr, 1qaa, 1jey, 1nk2, ... tau, 5gat, 1qrv, 1a73, 2gat and 1j1v), TF/DNA refers to remaining 21 transcription factor complexes (including 1lmb, 1cma, 1apl, 1par, 1run, 1glu, 1nfk, 1efa, 1mdy, 1tsr, 1ipp, 1ytf, 1vkx, 1oct, 1ihf, 1bc7, 1aay, 1cez, 1yrn, 1ysa and 1b3t).

Table 1 Data set of protein–DNA complexes Structural set (141 complexes) 1a02 1a0a 1a1g 1a1h 1a1k 1a3q 1akh 1am9 1an2 1an4 1apl 1au7 1b01 1b3t 1b72 1b8i 1bc8 1bdt 1bf5 1bl0 1by4 1c0w 1c9b 1cdw 1cez 1cf7 1cgp 1cit 1d3u 1d5y 1ddn 1dh3 1du0 1dux 1e3o 1ea4 1efa 1egw 1f2i 1f5t 1fjl 1fos 1fzp 1g2f 1gd2 1gji 1gt0 1gu4 1gu5 1gxp 1h6f 1h8a 1h9d 1h9t 1hbx 1hcq 1hlo 1hlz 1hw2 1hwt 1ic8 1if1 1ig7 1ign 1imh 1io4 1j59 1je8 1jfi 1jgg 1jj4 1jk1 1jk2 1jnm 1jt0 1k6o 1k78 1k79 1k7a 1kb2 1kb4 1kb6 1ku7 1l3l 1lat 1lb2 1le5 1le9 1llm 1lmb 1lq1 1mdy 1mhd 1mjm 1mjo 1mm8 1mnm 1mnn 1mur 1n6j 1ngm 1nkp 1nvp 1nwq 1oct 1odh 1owf 1p47 1p7h 1pdn 1per 1pp7 1pp8 1pue 1puf 1pyi 1pzu 1r0o 1r4o 1r4r 1ram 1rio 1rpe 1run 1skn 1tf6 1tgh 1tsr 1ubd 1yrn 1ysa 1ytb 1ytf 2cgp 2drp 2gli 2hap 2hdd 2or1 6cro 6pax Table 2 Recognition accuracy for specific interactions between TFs and native bound DNA sequences Accuracy Top 1(%) Top 10(%) Top 20(%) Top 1(%) Top 5(%) Whole structural set 39.7 70.2 77.3 79.4 90.1 α-Helix a 26.3 54.4 63.2 66.7 82.5 α-Helix + β-strand a 49.4 79.2 85.7 87.0 94.8 a α-helix and β-strand refer to the secondary structures of DNA-binding sites.

Publication Year: 2005