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PDB ID Mentions in PubMed Central Article count: 23

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PDB ID Mentions in PubMed Central

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Detecting DNA-binding helix-turn-helix structural motifs using sequence and structure information.

(2005) Nucleic Acids Res 33

PubMed: 15831786 | PubMedCentral: PMC1079965 | DOI: 10.1093/nar/gki349

The figure shows the multiple alignments and the DNA-binding domains of two HTH protein families from the Pfam database ( 24 ), the family of the trp operon repressor (UniProt code TRPR_ECOLI; PDB cod... 1JHG, chain A) and the family of the lambda repressor/operator (UniProt code RPC1_LAMBD; PDB code 1LMB, chain 3).

Table 1 List of protein families and corresponding templates composing set1 Protein name PDB ID Pfam ID UniProt ID Homeobox protein Hox-B1 1B72 Homeobox PBX1_HUMAN Molybdate-dependent transcription regulator (Mode) 1B9M HTH_1 MODE_ECOLI Multiple antibiotic resistance protein (Mara) 1BL0 HTH_AraC MARA_ECOLI Transcription factor Mbp1 1BM8 APSES MBP1_YEAST Gere regulatory protein 1FSE GerE GERE_BACSU Hin recombinase 1HCR HTH_7 HIN_SALTY Major centromere autoantigen B 1HLV CENP-B-N CENB_HUMAN Camp receptor protein 1HW5 Crp CRP_ECOLI Trp operon repressor 1JHG Trp_repressor TRPR_ECOLI Lambda repressor/operator complex 1LMB HTH_3 RPC1_LAMBD Purine nucleotide synthesis repressor 1QPZ lacI PURR_ECOLI Transcriptional repressor Smtb 1SMT HTH_5 SMTB_SYNP7 Diphtheria toxin repressor 2DTR Fe_dep_repress DTXR_CORDI Tetracycline repressor 2TCT tetR TER4_ECOLI Table 2 Jackknifed prediction results at different SAM entropy values HMM rep structure fw 0.3 a fw 0.5 a fw 0.7 a fw 0.8 a fw 1.0 a 1B72 0 0 0 0 0 1B9M 0 0 0 0 0 1BL0 0 0 0 1 1 1BM8 0 0 0 0 0 1FSE 2 2 1 1 0 1HCR 2 3 4 4 3 1HLV 2 5 6 6 6 1HW5 0 2 3 3 2 1JHG 0 0 0 0 0 1LMB 2 8 10 8 8 1QPZ 4 5 5 5 4 1SMT 3 3 3 3 3 2DTR 2 3 3 3 3 2TCT 2 7 8 8 7 Total hits 19 38 43 42 37 a fw indicates the entropy value used to derive HMMs from FD multiple alignments.

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 1 Experimental binding affinity dataset Name PDB code Method (Res., Å) ΔΔ G data points Organism Reference Zif268 1aay X-ray (1.6) 15 (8) Mus musculus ( 42 ) Zif268 1aay X-ray (1.6) 6 (6) M.musculus ( 67 ) Zif268 D20A 1jk1 X-ray (1.9) 6 (6) M.musculus ( 67 ) Tus 1ecr X-ray (2.7) 20 (20) Escherichia coli ( 68 ) LacR 1efa X-ray (2.6) 5 (5) E.coli ( 69 ) λR 1lmb X-ray (1.8) 51 (51) λ-Phage ( 51 ) TrpR 1tro X-ray (1.9) 9 (9) E.coli ( 70 ) ER 1hcq X-ray (2.4) 7 (7) Homo sapiens ( 71 ) CroR 6cro X-ray (3.0) 56 (56) λ-Phage ( 52 ) EcoRI 1ckq X-ray (1.85) 13 (13) E.coli ( 41 ) Crp 1run X-ray (2.7) 15 (15) E.coli ( 72 ) BamHI 1bhm X-ray (2.2) 23 (0) Bacillus amyloliquefaciens ( 49 ) PU.1 ETS 1pue X-ray (2.1) 25 (0) M.musculus ( 50 ) Ndt80 1mnn X-ray (1.4) 26 (0) Saccharomyces cerevisiae ( 34 ) MAT a 1/α2 1yrn X-ray (2.5) 54 (0) S.cerevisiae ( 30 ) c-Myb 1mse NMR (NA) 27 (0) M.musculus ( 47 ) AtERF1 1gcc NMR (NA) 21 (0) Arabidopsis thaliana ( 45 ) For protein–DNA structures solved by X-ray crystallography, resolution (Å) is shown in parentheses.

Publication Year: 2005


FOLD-RATE: prediction of protein folding rates from amino acid sequence.

(2006) Nucleic Acids Res 34

PubMed: 16845101 | PubMedCentral: PMC1538837 | DOI: 10.1093/nar/gkl043

( a ) First page showing the input format (amino acid sequence in single letter code; an example is shown for λ repressor (1LMB) and structural class information (all-α).

Publication Year: 2006


Energetics of the protein-DNA-water interaction.

(2007) BMC Struct Biol 7

PubMed: 17214883 | PubMedCentral: PMC1781455 | DOI: 10.1186/1472-6807-7-4

regulator Homeodomain Helix-turn-helix 1.10.10.60 [97] 1lmb Lambda repressor Transcr.

Publication Year: 2007


Energetics of protein-DNA interactions.

(2007) Nucleic Acids Res 35

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

The training set includes all structures in the dataset (Supplemental Materials) except the nine structures in the testing set (1a02, 1a3q, 1ckq, 1ecr, 1lmb, 1run, 6cro).

The full set includes 189 mutants from ten structures: 1aay, 1ckq, 1ecr, 1efa, 1hcq, 1jk1, 1lmb, 1run, 1tro and 6cro.

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


Catalytic domain of restriction endonuclease BmrI as a cleavage module for engineering endonucleases with novel substrate specificities.

(2007) Nucleic Acids Res 35

PubMed: 17855396 | PubMedCentral: PMC2094064 | DOI: 10.1093/nar/gkm665

The absence of divalent ions in the λ repressor-target DNA structure (PDB entry 1LMB) and the decrease in ‘star’ activity of wild-type BmrI in the presence of magnesium ions (u... published data) support the notion that magnesium ions increase specific cleavage activity of the fusion protein by inhibiting DNA cleavage activity of the BmrI DNA cleavage domain.

Publication Year: 2007


Identification of DNA-binding protein target sequences by physical effective energy functions: free energy analysis of lambda repressor-DNA complexes.

(2007) BMC Struct Biol 7

PubMed: 17900341 | PubMedCentral: PMC2194778 | DOI: 10.1186/1472-6807-7-61

Methods Model building Atomic coordinates of the λ repressor dimer bound to O L 1 DNA operator were taken from the 1.8 Å resolution X-ray crystal structure deposited in the Protein Dat... Bank [ 77 ] (PDB code 1LMB).

Publication Year: 2007


DNA conformations and their sequence preferences.

(2008) Nucleic Acids Res 36

PubMed: 18477633 | PubMedCentral: PMC2441783 | DOI: 10.1093/nar/gkn260

The PDB codes of the structures used in the analysis Structure Type PDB Codes Noncomplexed A-DNA ( 46 ) 118d, 137d, 138d, 160d, 1d78, 1d79, 1dnz, 1kgk, 1m77, 1ma8, 1mlx, 1nzg, 1vj4, 1xjx, 1z7i, 1zex, ... zey, 1zf1, 1zf6, 1zf8, 1zf9, 1zfa, 213d, 243d, 260d, 295d, 2d94, 317d, 338d, 344d, 345d, 348d, 349d, 368d, 369d, 370d, 371d, 395d, 396d, 399d, 414d, 440d, 9dna, dh010, adh012, adh034 Noncomplexed B-DNA ( 72 ) 122d, 123d, 158d, 183d, 196d, 1bd1, 1bna, 1cw9, 1d23, 1d3r, 1d49, 1d56, 1d61, 1d8g, 1d8x, 1dou, 1dpn, 1edr, 1ehv, 1en3, 1en8, 1en9, 1ene, 1enn, 1fq2, 1g75, 1i3t, 1ikk, 1j8l, 1jgr, 1l4j, 1l6b, 1m6g, 1n1o, 1nvn, 1nvy, 1p4y, 1p54, 1s23, 1s2r, 1sgs, 1sk5, 1ub8, 1ve8, 1zf0, 1zf3, 1zf4, 1zf5, 1zf7, 1zfb, 1zff, 1zfg, 232d, 251d, 2d25, 307d, 355d, 3dnb, 403d, 423d, 428d, 431d, 436d, 454d, 455d, 456d, 460d, 463d, 476d, 477d, 5dnb, 9bna DNA/drug and DNA/ protein complexes, Z-DNA, quadruplexes (329) 110d, 115d, 131d, 145d, 151d, 152d, 159d, 181d, 182d, 184d, 190d, 191d, 1a1g, 1a1h, 1a1i, 1a1k, 1a2e, 1a73, 1aay, 1ais, 1azp, 1b94, 1b97, 1bf4, 1bqj, 1brn, 1c8c, 1cdw, 1ckq, 1cl8, 1cn0, 1d02, 1d11, 1d14, 1d15, 1d21, 1d22, 1d2i, 1d32, 1d37, 1d38, 1d40, 1d41, 1d45, 1d48, 1d53, 1d54, 1d58, 1d67, 1d76, 1d90, 1d9r, 1da0, 1da2, 1da9, 1dc0, 1dc1, 1dcg, 1dcr, 1dcw, 1dfm, 1dj6, 1dl8, 1dn4, 1dn5, 1dn8, 1dnf, 1dp7, 1dsz, 1e3o, 1egw, 1em0, 1emh, 1eo4, 1eon, 1esg, 1eyu, 1f0v, 1fd5, 1fdg, 1fhz, 1fiu, 1fms, 1fn1, 1fn2, 1g2f, 1g9z, 1gtw, 1gu4, 1h6f, 1hcr, 1hlv, 1hwt, 1hzs, 1i0t, 1i3w, 1ick, 1ign, 1ih4, 1ih6, 1imr, 1ims, 1j59, 1j75, 1jb7, 1jes, 1jft, 1jh9, 1jk1, 1jk2, 1jpq, 1jtl, 1juc, 1jux, 1jx4, 1k3w, 1k3x, 1k9g, 1kbu, 1kci, 1kx3, 1kx5, 1l1h, 1l1t, 1l1z, 1l3l, 1l3s, 1l3t, 1l3u, 1l3v, 1lat, 1lau, 1ljx, 1llm, 1lmb, 1m07, 1m19, 1m3q, 1m5r, 1m69, 1m6f, 1mf5, 1mj2, 1mjm, 1mjo, 1mjq, 1mnn, 1mus, 1mw8, 1nh2, 1njw, 1njx, 1nk0, 1nk4, 1nk7, 1nk8, 1nk9, 1nkc, 1nke, 1nkp, 1nnj, 1nqs, 1nr8, 1nt8, 1nvp, 1o0k, 1omk, 1orn, 1p20, 1p3i, 1p3l, 1p71, 1per, 1pfe, 1ph4, 1ph6, 1ph8, 1pji, 1pjj, 1puf, 1pup, 1puy, 1q3f, 1qda, 1qn3, 1qn4, 1qn5, 1qn6, 1qn8, 1qn9, 1qna, 1qnb, 1qne, 1qum, 1qyk, 1qyl, 1qzg, 1r2z, 1r3z, 1r41, 1r68, 1rff, 1rh6, 1rnb, 1rpe, 1rqy, 1run, 1s1k, 1s1l, 1s32, 1ssp, 1suz, 1sx5, 1sxq, 1t9i, 1tdz, 1tez, 1tro, 1u1p, 1u1q, 1u1r, 1u4b, 1ue2, 1ue4, 1uhy, 1v3n, 1v3o, 1v3p, 1vzk, 1w0u, 1wd0, 1wte, 1wto, 1wtp, 1wtq, 1wtr, 1wtv, 1xa2, 1xam, 1xc9, 1xjv, 1xo0, 1xuw, 1xux, 1xvn, 1xvr, 1xyi, 1ytb, 1ytf, 1zez, 1zf2, 1zna, 200d, 210d, 211d, 212d, 215d, 221d, 224d, 234d, 235d, 236d, 241d, 242d, 244d, 245d, 254d, 258d, 276d, 277d, 278d, 279d, 284d, 288d, 292d, 293d, 2bdp, 2bop, 2cgp, 2crx, 2dcg, 2des, 2hap, 2hdd, 2nll, 2or1, 2pvi, 304d, 306d, 308d, 313d, 314d, 331d, 334d, 336d, 351d, 352d, 360d, 362d, 366d, 367d, 383d, 385d, 386d, 3bam, 3bdp, 3cro, 3crx, 3hts, 3pvi, 400d, 417d, 427d, 432d, 441d, 442d, 443d, 452d, 453d, 465d, 467d, 473d, 481d, 482d, 4bdp, adh013, zdf013, zdfb03, zdfb06 The DNA conformational space was investigated at the level of a dinucleotide unit with its 5′-end phosphate group removed; it was described by six backbone torsion angles between γ and δ + 1, plus two χ angles characterizing the glycosidic bond ( Figure 1 ).

Publication Year: 2008


Assessment of the optimization of affinity and specificity at protein-DNA interfaces.

(2009) Nucleic Acids Res 37

PubMed: 19389725 | PubMedCentral: PMC2691843 | DOI: 10.1093/nar/gkp242

MATERIALS AND METHODS Structural data The following high-resolution crystal structures of protein–DNA complexes were modeled: Helical transcription factors: 1ig7 1k61 1puf 2hdd 1w0u 1e3o 2d5v ... zaa 1ubd 1g2f 1am9 1gd2 1gu4 1jnm 2dgc 1nkp 1lmb 2or1 1hcr 1ign 1tc3 1bl0 1zs4 2h27 1r71 1pp7 1bc8 1dp7 1f4k.

Publication Year: 2009


PROTDES: CHARMM toolbox for computational protein design.

(2008) Syst Synth Biol 2

PubMed: 19572216 | PubMedCentral: PMC2735645 | DOI: 10.1007/s11693-009-9026-7

 3 Structure of the DNA-protein interaction region of cI protein: the original structure, [PDB:1LMB] that shows the two H-bonds formed between Q44 and A4 Fig.

We have considered the 1.8 Å resolution structure [PDB:1LMB] (Beamer and Pabo 1992 ) and analyzed the DNA-protein binding region, shown in Fig.

Publication Year: 2008


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

We select PDB 1LMB:4 as an example to show how the predicted binding mode information can be used to enhance the binding residues prediction.

Figure 2 displays the prediction result of PDB ID 1LMB:4 , which is a difficult case in our binding residues prediction experiment.

The protein, 1LMB:4 , belongs to the HTH_3 domain which is classified in the group of helix-turn-helix, which has 10 sequence-specific binding residues and 18 non-specific binding residues.

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:B 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 ].

The binding mode predictor can correctly classify the 1LMB:4 into helix-turn-helix group.

Figure 2 A difficult case (PDB ID 1LMB:4 ) of binding residue prediction, which can be enhanced with the best aligned template of correct predicted protein-DNA binding mode .

The protein-DNA binding mode prediction is also proposed in this framework, and we select 1LMB:4 as an example to reveal how can be helpful for improving DNA-binding residue prediction.

Publication Year: 2009


Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

(2010) PLoS Comput Biol 6

PubMed: 20221255 | PubMedCentral: PMC2832674 | DOI: 10.1371/journal.pcbi.1000694

The structure of the folded state of λ 6-85 was taken from its crystal structure in complex with operator DNA (pdbcode: 1LMB [103] ); the G46A & G48A mutations present ... n the experimental construct were made using the rotamer-sampling method SCWRL3 [104] .

Publication Year: 2010


Integration of open access literature into the RCSB Protein Data Bank using BioLit.

(2010) BMC Bioinformatics 11

PubMed: 20429930 | PubMedCentral: PMC2880030 | DOI: 10.1186/1471-2105-11-220

of Articles 1JJ2 Large Ribosomal Subunit 27 1J5E 30S Ribosomal Subunit 19 1FFK Large Ribosomal Subunit 19 1LMB Lambda Repressor 19 1AAY Zinc Finger 17 1TSR P53 16 1F88 Rhodopsin 15 1BRS Barnase/Barsta... complex 14 The open access literature for RCSB PDB entries is available from the Literature tab for each structure entry at http://www.rcsb.org .

Publication Year: 2010


Calculation of accurate small angle X-ray scattering curves from coarse-grained protein models.

(2010) BMC Bioinformatics 11

PubMed: 20718956 | PubMedCentral: PMC2931518 | DOI: 10.1186/1471-2105-11-429

PDBcode Chain Length Rg S 1HCR A 52 6.92 0.504 1TGS I 56 6.25 0.137 1TGX A 60 6.84 0.158 1ISU A 62 6.02 0.203 1BF4 A 63 6.44 0.223 1PCF A 66 8.33 0.160 1B3A A 67 7.27 0.122 1ATZ A 75 7.24 0.214 1DP7 P... 76 7.35 0.237 3HTS B 82 7.02 0.286 3EIP A 84 7.35 0.233 2BOP A 85 7.90 0.122 1LMB 4 92 7.88 0.235 1FLT Y 94 7.55 0.132 1DIF A 99 7.82 0.260 1IIB A 103 7.38 0.228 1CMB A 104 8.35 0.116 256B A 106 8.37 0.245 1EVH A 111 7.78 0.180 1DPT A 117 8.56 0.194 1FLM B 122 8.26 0.118 2BBK L 124 8.05 0.317 1NWP A 128 7.88 0.179 1BBH A 131 9.18 0.161 1AQZ A 142 8.48 0.208 1A3A D 144 8.15 0.230 1M6P A 146 8.70 0.141 2TNF A 148 9.71 0.252 1ELK A 153 8.62 0.369 1NBC A 155 8.53 0.262 1DPS D 156 9.82 0.272 1PHN A 162 10.48 0.204 1C02 A 166 9.60 0.230 1YTB A 180 11.73 0.190 1BEH B 183 8.78 0.204 1ATL A 200 9.30 0.267 1BSM A 201 10.05 0.191 1YAC B 204 9.80 0.248 6GSV B 217 10.11 0.203 1AUO A 218 9.34 0.137 1QL0 A 241 9.59 0.165 1CYD A 242 10.13 0.287 1TPH 1 245 9.87 0.169 1A28 B 249 10.39 0.300 1C90 A 265 10.30 0.142 1AQU A 281 10.73 0.177 1BF6 B 291 10.21 0.294 1FTR A 296 12.14 0.295 4PGA A 330 11.67 0.217 1CZF A 335 11.43 0.241 S is the difference between the curves resulting from the two-body model and CRYSOL in units of "experimental" standard deviations.

Publication Year: 2010


Benchmarks for flexible and rigid transcription factor-DNA docking.

(2011) BMC Struct Biol 11

PubMed: 22044637 | PubMedCentral: PMC3262759 | DOI: 10.1186/1472-6807-11-45

(Å) SCOP Protein Oligo_state DNA NRBC b BSA(Å 2 ) c ZIF268 1aay 1.60 g.37.1.1 A Monomer B, C 13 960.81 Max 1an2 2.90 a.38.1.1 A, C Homodimer B, D 10 933.75 Papillomavirus E2 1jj4 2.40 ... .58.8.1 A, B Heterodimer C, D 10 839.96 QacR 1jt0 a 2.90 a.4.1.9 B, D Homodimer E, F 12 1085.51 Lambda repressor 1lmb 1.80 a.35.1.2 3, 4 Homodimer 1, 2 10 1105.4 TATA-binding 1qn4 1.86 d.129.1.1 B Monomer E, F 15 1107.51 Tet repressor 1qpi 2.50 a.4.1.9 A, C Homodimer B, M 14 973.49 MecI 1sax 2.80 a.4.5.39 A, B Homodimer C, D 12 1130.16 Trep repressor 1tro a 1.90 a.4.12.1 A, C Homodimer I, J 12 1243.06 OhrR 1z9c 2.64 a.4.5.28 C, D Homodimer I, J 12 1669.81 Easy Phi lambda phage cII 1zs4 1.70 a.39.1.9 A, B, C, D HT d U, T 14 1043.06 p53 2ac0 1.80 b.2.5.2 A, B, C, D HT d E, F, G, H 21 1921.76 CAP 2cgp 2.20 a.4.5.4 A, F Homodimer B, C, D, E 10 944.43 LRP/ASNC family protein 2e1c 2.10 a.4.5.32 A, F Homodimer B, D 11 803.23 IdeR 2it0 a 2.60 a.4.5.24 C, D Homodimer E, F 11 1123.8 Phi 434 repressor 2or1 2.50 a.35.1.2 R, L Homodimer A, B 17 1021.78 CgmR 2yvh a 2.50 N/A C, D Homodimer E, F, G, H 10 1056.55 Controller protein 3clc a 2.80 a.35.1.3 C, D Homodimer E, F 14 1002.57 HipB 3dnv 2.68 N/A B, C Homodimer E, T 10 990.24 CprK 3e6c 1.80 a.4.5.4 C, D Homodimer A, B, E, F 12 1059.42 NrtR 3gz6 2.90 N/A A, B Homodimer C, D 15 1845.4 CopG repressor 1b01 2.56 a.43.1.3 A, B Homodimer E, F 5 573.31 RXR-alpha 1by4 2.10 g.39.1.2 A, B Homodimer E, F 8 1031.94 Met repressor 1cma 2.80 a.43.1.5 A, B Homodimer C, D 4 693.13 PhoB 1gxp a 2.50 a.4.6.1 A Monomer C, D 7 739.09 Myb 1h8a a 2.23 a.4.1.3 C Monomer D, E 8 738.59 AML1 Runt domain 1hjc 2.65 b.2.5.6 D Monomer E, F 6 540.76 MtaN 1r8d 2.70 a.6.1.3 A, B Homodimer C, D 8 1338.92 Hard Sigma subunit domain 4 1rio a 2.30 a.4.13.2 H Monomer U, T 6 423.27 Prospero 1xpx 2.80 a.4.1.1 A Monomer C, D 3 325.79 Put3 1zme 2.50 g.38.1.1 C, D Homodimer A, B 5 1211.56 Omega repressor 2bnw 2.45 a.43.1.4 A, B Homodimer E, F 4 519.26 ILF 2c6y 2.40 a.4.5.14 A Monomer C, D 8 814.94 Phi 29 protein p4 2fio 2.70 N/A A, B Homodimer C, D 4 903.33 IRF-2 2irf a 2.20 a.4.5.23 L Monomer C, D 6 668.45 PutA 2rbf 2.25 N/A A, B Homodimer C, D 8 614.12 SoxR 2zhg 2.80 a.6.1.3 A, D Homodimer B, C 6 869.73 Engrailed homeodomain 3hdd a 2.20 a.4.1.1 A Monomer C, D 4 524.73 a Has more than one binding unit b NRBC: number of protein residues having side-chain contacts with DNA bases c BSA: buried surface area in TF-DNA complexes d HT: homotetramer Results Overview of benchmark test cases There are a total of 38 test cases for our TF-DNA docking benchmarks.

(Å) SCOP Protein Oligo_state DNA CopG repressor 1b01 2.56 a.43.1.3 A, B Homodimer E, F 5 2cpg 1.60 A, B 0.511 0.460 PhoB 1gxp a 2.50 a.4.6.1 A Monomer C, D 7 1gxq 2.00 A 1.622 1.622 AML1 Runt domain 1hjc 2.65 b.2.5.6 D Monomer E, F 6 1ean 1.70 A 1.056 1.056 Papillomavirus E2 1jj4 2.40 d.58.8.1 A, B Heterodimer C, D 10 1f9f 1.90 C, D 0.949 1.484 TATA-binding protein 1qn4 1.86 d.129.1.1 B Monomer E, F 15 1vok 2.10 B 0.934 0.934 Tet repressor 1qpi 2.50 a.4.1.9 A, C Homodimer B, M 14 2tct 2.10 A, B 2.061 1.359 MtaN 1r8d 2.70 a.6.1.3 A, B Homodimer C, D 8 1jbg 2.75 A, B 2.107 1.368 Sigma subunit domain 4 1rio a 2.30 a.4.13.2 H Monomer U, T 6 1ku3 1.80 A 1.405 1.405 Easy MecI 1sax 2.80 a.4.5.39 A, B Homodimer C, D 12 1okr 2.40 A, B 1.718 1.586 CAP 2cgp 2.20 a.4.5.4 A, F Homodimer B, C, D, E 10 1i5z 1.90 A, B 1.652 1.919 LRP/ASNC family protein 2e1c 2.10 a.4.5.32 A, F Homodimer B, D 12 2zny 2.59 A, B 1.339 1.184 IdeR 2it0 a 2.60 a.4.5.24 C, D Homodimer E, F 11 2isy 1.96 A, B 0.476 0.489 Phi 434 repressor 2or1 2.50 a.35.1.2 R, L Homodimer A, B 17 1r69 c 2.00 A, B 0.570 0.493 PutA 2rbf 2.25 N/A A, B Homodimer C, D 8 2gpe 1.90 A, B 0.798 0.571 SoxR 2zhg 2.80 a.6.1.3 A, D Homodimer B, C 6 2zhh 3.20 A, B 1.749 1.467 Controller protein 3clc a 2.80 a.35.1.3 C, D Homodimer E, F 14 3fya 3.00 A, B 0.834 0.809 CprK 3e6c 1.80 a.4.5.4 C, D Homodimer A, B, E, F 12 3e5u 1.83 A, B 1.060 0.906 NrtR 3gz6 2.90 N/A A, B Homodimer C, D 15 3gz5 2.20 A, B 0.853 0.726 Max 1an2 2.90 a.38.1.1 A, C Homodimer B, D 10 1r05 d N/A A, B 8.074 4.767 RXR-alpha 1by4 2.10 g.39.1.2 A, B Homodimer E, F 8 1rxr c, d N/A A, B 4.637 2.326 Met repressor 1cma 2.80 a.43.1.5 A, B Homodimer C, D 4 1cmc 1.80 A, B 2.232 2.313 Myb 1h8a a 2.23 a.4.1.3 C Monomer D, E 8 1gv2 1.68 A 9.153 9.153 QacR 1jt0 a 2.90 a.4.1.9 B, D Homodimer E, F 12 1jt6 2.54 D, E 2.924 1.650 Lambda repressor 1lmb 1.80 a.35.1.2 3, 4 Homodimer 1, 2 10 1lrp 3.20 A, B 32.342 0.928 Trp repressor 1tro a 1.90 a.4.12.1 A, C Homodimer I, J 12 1p6z 1.67 N, R 3.095 1.427 Prospero 1xpx 2.80 a.4.1.1 A Monomer C, D 3 1mij 2.05 A 0.519 0.519 Hard OhrR 1z9c 2.64 a.4.5.28 C, D Homodimer I, J 12 1z91 2.50 A, B 2.521 1.919 Put3 1zme 2.50 g.38.1.1 C, D Homodimer A, B 5 1ajy d N/A A, B 9.326 8.725 Phi lambda phage cII 1zs4 1.70 a.35.1.9 A, B, C, D HT f U, T 14 1zpq 2.80 A, B, C, D 4.947 2.679 p53 2ac0 1.80 b.2.5.2 A, B, C, D HT f E, F, G, H 21 2j1y 1.69 A, B, C, D 25.325 0.932 Omega repressor 2bnw 2.45 a.43.1.4 A, B Homodimer E, F 4 1irq 3.50 A, B 0.887 1.049 ILF 2c6y 2.40 a.4.5.14 A Monomer C, D 8 1jxs d N/A A 2.830 2.830 Phi 29 protein p4 2fio 2.70 N/A A, B Homodimer C, D 4 2fip 2.00 C, D 0.679 0.496 IRF-2 2irf a 2.20 a.4.5.23 L Monomer C, D 6 1irf d N/A A 3.459 3.459 CgmR 2yvh a 2.50 N/A C, D Homodimer E, F, G, H 10 2yve 1.40 A, B 2.663 1.599 HipB 3dnv 2.68 N/A B, C Homodimer E, T 10 2wiu 2.35 B, D 3.511 2.925 Engrailed homeodomain 3hdd a 2.20 a.4.1.1 A Monomer C, D 4 1enh 2.10 A 0.716 0.716 a Has more than one binding unit b NRBC: number of protein residues having side-chain contacts with DNA bases c Modeled unit structure d NMR structure, resolution N/A e RMSD u : global RMSD between bound and unbound TF-units, RMSD c : global RMSD between bound and unbound TF-chains f HT: homotetramer Table 2 Rigid TF-DNA docking benchmark TF-DNA Complex Name PDB TF-DNA Unit Chains ID Res.

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.

Publication Year: 2012


Determinants of bacteriophage 933W repressor DNA binding specificity.

(2012) PLoS One 7

PubMed: 22509323 | PubMedCentral: PMC3317979 | DOI: 10.1371/journal.pone.0034563

In brief, the sequence of 933WR NTD (residues 1–75) was aligned against three template structures; the NTD's of lambda repressor (1LMB); P22 repressor (1ADR) and 434 repressor (2OR1) using Clu... talW [17] .

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


Observation of complete pressure-jump protein refolding in molecular dynamics simulation and experiment.

(2014) J Am Chem Soc 136

PubMed: 24437525 | PubMedCentral: PMC3985862 | DOI: 10.1021/ja412639u

The initial structure of the λ-repressor fragment was taken from the Protein Data Bank (PDB code 1LMB).

Publication Year: 2014


TSpred: a web server for the rational design of temperature-sensitive mutants.

(2014) Nucleic Acids Res 42

PubMed: 24782523 | PubMedCentral: PMC4086094 | DOI: 10.1093/nar/gku319

The proteins were gene V (PDB: 1YHA), lambda repressor (PDB: 1LMB), T4 Lysozyme (PDB: 2LZM), CcdB (PDB: 3VUB), Gal4 (PDB: 3CQQ) and Ura3 (PDB: 1DQW)) ( 13 , 23 , 44–49 ).

Ts mutant position as predicted by sequence-based, structured-based or both methods Protein PDB ID Chain length Residue position Residue type Prediction method gene V 1YHA 87 35 VAL Both 45 VAL Both 47 ILE Structure 63 VAL Structure 81 LEU Structure 78 ILE Sequence lambda repressor 1LMB 92 51 PHE Both 65 LEU Both 76 PHE Both 84 ILE Both 18 LEU Structure 36 VAL Structure 47 VAL Structure T4 lysozyme 2LZM 164 6 MET Both 102 MET Both 149 VAL Structure 153 PHE Structure 103 VAL Sequence CcdB 3VUB 101 17 PHE Both 18 VAL Both 33 VAL Both 34 ILE Both 54 VAL Both 5 VAL Structure 36 LEU Structure 63 MET Structure 50 LEU Sequence 53* VAL Sequence 96 LEU Sequence 97 MET Sequence 98 PHE Sequence Gal4 3COQ 88 68 PHE Both 69 LEU Sequence 70 LEU Sequence Ura3 1DQW 267 25 MET Structure 32 LEU Structure 118 ILE Structure The wild-type residue (three-letter amino acid code) at the position is listed under residue type.

Publication Year: 2014


Specificity and affinity quantification of flexible recognition from underlying energy landscape topography.

(2014) PLoS Comput Biol 10

PubMed: 25144525 | PubMedCentral: PMC4140643 | DOI: 10.1371/journal.pcbi.1003782

In details, the first three dimers (PDB: 1cop, 1lmb, 1lfb) (Figure S1 in Text S1 ) are found to participate into the process of gene regulation [95] – [97] , in which flexibility can lead to f... st association/dissociation rates and thus highly efficient function.

g001 Figure 1 The binding affinity (stability) for rigid (independent) and flexible (effective) binding shown in (A) heat capacity curves and (B) free energy landscapes for Lambda Cro repressor (PDB: 1cop) and Lambda repressor (PDB: 1lmb).

Publication Year: 2014


Tetrameric c-di-GMP mediates effective transcription factor dimerization to control Streptomyces development.

(2014) Cell 158

PubMed: 25171413 | PubMedCentral: PMC4151990 | DOI: 10.1016/j.cell.2014.07.022

First, BldD DNA binding domain-DNA complex models were constructed based on the SinR-DNA (PDB code 3ZKC ) or λ repressor-DNA (PDB code 1LMB ) complex structures and used in the MR program Phas... r ( McCoy et al., 2007 ).

Publication Year: 2014


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