Binding sites
Multiple protein-binding sites in an intracisternal A particle long terminal repeat.
... Three of the DNase I footprints include a sequence with homology to the simian virus 40 core enhancer and sequence motifs that closely resemble the binding sites for transcription factor[r] ...
8
DNA Replication Efficiency Depends on Transcription Factor-Binding Sites
... factor-binding sites in the regulatory region of variants help determine their rep- lication ...Sp1 sites was duplicated (as occurs during the naturally arising evolution of variants from serial ...
8
Identification of transcription factor binding sites using ATAC seq
... ChIP-seq of TFs and motif-predicted binding sites (MPBSs) were used as ground truth to evaluate the foot- printing prediction in this work following [8, 27]. We used here peaks from 124 TF ChIP-seq datasets ...
21
Angiotensin II binding sites in individual segments of the rat nephron
... hormone binding in discrete tubule segments, we determined the binding sites of 125I- angiotensin II along the nephron of Sprague-Dawley ...Specific binding in proximal convoluted tubule (PCT) ...
5
Deconstructing the DGAT1 enzyme: membrane interactions at substrate binding sites
... substrate binding sites of DGAT1 ...potential binding region for this substrate. Both these binding sites are proposed to lie within an extramembranous loop of the ...
15
Genome-wide mapping of Hif-1α binding sites in zebrafish
... Hif-1α binding sites in vhl mutant samples (5177), we were concerned that this could lead to a high number of false associa- tions with genes in their ...Hif-1α binding peaks within ±1Kb of their ...
17
Prediction of DNA-Binding Proteins and their Binding Sites
... DNA- binding residues is not only important for biological research (function annotation) but also for understanding pathogenesis of many ...interaction sites have been studied through biochemical ...
53
Genomic mapping of Suppressor of Hairy wing binding sites in Drosophila
... To explore Su(Hw) function we investigated the transcrip- tional consequences of lack of Su(Hw) using genome-wide microarray analysis. Examining gene expression changes in su(Hw) null mutant larvae and wing discs, we ...
16
Probing the Hotspot Binding Sites of Proteins: P22TSP, Ras and BAF.
... sugar binding pockets when the active site is ...active sites even when the proteins interact with different size sugar moieties such as P22TSP (octasaccharide or greater) and Lysozyme ...
190
Why Transcription Factor Binding Sites Are Ten Nucleotides Long
... We also analyzed systematic data on the transcription networks of S. cerevisiae and E. coli and discovered that transcription factors with a larger number of true targets tend to have less total information content (I n) ...
23
Mapping of Vps21 and HOPS Binding Sites in Vps8 and Effect of Binding Site Mutants on Endocytic Trafficking
... membrane binding regions could be mapped to the N-terminal part of the ...HOPS binding sites were mapped in ...complex binding had a strong effect on the turnover of the endocytic cargo ...
9
Large-Scale Analysis of Protein-Ligand Binding Sites using the Binding MOAD Database.
... the Binding MOAD database, a vast, curated set of protein-ligand complexes, for frequently observed patterns of binding-site composition with respect to ligand ...emerging binding-site prediction and ...
179
Mapping the 3D structures of small molecule binding sites
... protein–ligand binding sites that do not have ligands known to bind, we have incorporated fpocket cavity detection software and assessed the impact of this inclusion on BSC ...potential binding ...
13
Mapping genome-wide transcription factor binding sites in frozen tissues
... genome-wide binding profiles using chromatin from as lit- tle as ≈675,000 ...of binding sites that were shared even between 5 mg biological replicates (Additional file 1: Table ...of binding ...
10
Multiple transcription factor binding sites mediate adenovirus E1A transactivation.
... To avoid the complications inherent in studying early adenovirus promoters which contain binding sites for multiple transcription factors implicated in ElA transactivation, we synthesize[r] ...
8
Characterization of two novel YY1 binding sites in the polyomavirus late promoter.
... oligonucleotides, and following 10 min of incubation at room temperature, pro- tein-DNA complexes were separated from free DNA by electrophoresis on a 5% nondenaturing polyacrylamide gel and visualized by ...
6
The good, the bad and the dubious: VHELIBS, a validation helper for ligands and binding sites
... with binding sites improve, the changes are very small, except for the reduction in atomic ...ligand binding sites are typically the most important part of a structure model, and much ...
9
Identification and Analysis of Papillomavirus E2 Protein Binding Sites in the Human Genome
... represent binding sites in ...p63-binding sites in the human genome, only 8% of the best and 1 to 3% of the typical motifs were bound by p63 in vivo and only 10 to 20% of the bound targets ...
10
Study of Protein Binding Sites on the GTPase RalA and the Sugar-binding Protein Hen Egg White Lysozyme
... to sites on the ...many sites on the protein are generally weak, usually occurring because the solvents are present in high ...few binding sites in our experiments signifies that ...
289
A short update on the structure of drug binding sites on neurotransmitter transporters
... putative binding pockets in the occluded conformation, and the contact between these two amino acids was interrupted in the open to out conformation (Figure ...two binding sites merge into one large ...
5