Primary Citation PubMed: 1865905
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Contribution of nucleosome binding preferences and co-occurring DNA sequences to transcription factor binding.
(2013) BMC Genomics 14
PubMed: 23805837 | PubMedCentral: PMC3700821 | DOI: 10.1186/1471-2164-14-428
( C ) Overlapping crystal structures for the nucleosome (PDB ID: 1AOI), GR (1R4O) and c-Jun|Fos (1FOS) showing GR can bind the nucleosome-occluded DNA while c-Jun|Fos has steric hindrances.
X-ray crystal structures of GR (PDB ID: 1R4O) and AP-1 (PDB ID: 1FOS) proteins bound to their canonical DNA motifs were overlaid with an X-ray structure of the histone octamer (PDB ID: 1AOI) bound to DNA (a nucleosome) using the program Chimera [ 31 ] to create a physical model of these proteins bound to the same DNA.
Publication Year: 2013
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
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
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