Binding-sites
Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure.
... previous binding site prediction algorithms have considered both sequence and ...functional sites [41], and Panchenko et ...functional sites by estimating the effect on structural stability of ...
18
CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex.
... genomic sites with our ChIP-array analysis of binding sites for another Drosophila insulator-binding protein, Su(Hw) ...consensus binding sites. In contrast to most ...
12
Transcription factor binding sites prediction based on modified nucleosomes.
... factor binding site (TFBS) ...actual binding sites, they usually produce a large number of false positive (FP) predictions and so are impoverished sources of ...start sites to distinguish true ...
10
Prediction of nucleosome positioning based on transcription factor binding sites.
... A number of studies have been performed in an attempt to determine nucleosome positioning signals at the level of TFs or transcription factor binding sites (TFBSs), which are bound by TFs to enable gene ...
7
Severe MgADP inhibition of Bacillus subtilis F1-ATPase is not due to the absence of nucleotide binding to the noncatalytic nucleotide binding sites.
... stalled. It is a common mechanism among all ATP synthases examined so far. Several factors are known to affect MgADP inhibition; Sodium azide stabilizes MgADP inhibition [6]: A detergent lauryldimethylamine N-oxide ...
5
A structural-based strategy for recognition of transcription factor binding sites.
... If a given factor has a well-characterized PWM, it is straightforward to identify potential TFBSs. However, if a well- characterized PWM does not exist, there are several strategies that can be followed. Furthermore, if ...
10
Exploring the composition of protein-ligand binding sites on a large scale.
... ligand binding site determines the interactions available for diffusion-mediated ligand binding, and understanding general composition of these sites is of great importance if we are to gain insight ...
14
Novel Phosphotidylinositol 4,5-Bisphosphate Binding Sites on Focal Adhesion Kinase.
... potential binding site suggested by our simulations, located near the interface between the N- and C-lobes of the kinase ...II binding sites are tightly correlated to the two basic patches on the ...
12
Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.
... AtMYB61 binding site with the TAC nucleotides in the ACCTAC sequence determine that these nucleotides are less essential for ...predicted binding sites of ...AtMYB61 binding site and the TAC ...
11
Adsorption of glyphosate in Chilean soils and its relationship with unoccupied phosphate binding sites (1)
... phosphate binding sites found for that ...phosphate binding sites were very much similar (Table ...phosphate sites for these two soils was ...
7
DNA-MATRIX: a tool for constructing transcription factor binding sites Weight matrix
... factor binding sites prediction in whole genome remains a challenge for the ...factor binding sites prediction tools required either direct pattern sequence or weight ...factor binding ...
3
Protective action of resveratrol in human skin: possible involvement of specific receptor binding sites.
... In summary, here we show that resveratrol possibly exerts its protective effect on epidermal cells by binding on specific polyphenol binding sites. Intracellular mechanisms underlying the protective ...
12
Expansion of GA Dinucleotide Repeats Increases the Density of CLAMP Binding Sites on the X-Chromosome to Promote Drosophila Dosage Compensation.
... start sites (TSS), the MSL complex is recruited to active gene bodies and transcription termination sites (TTS) to promote the progression of RNA Polymerase II across genes ...CLAMP binding motif ...
28
Differential Nucleosome Occupancies across Oct4-Sox2 Binding Sites in Murine Embryonic Stem Cells.
... Oct4/Sox2 binding sites within the genes of inter- est, we scanned the promoter and downstream regions of Oct4, Sox2, Pax6, Nes, Sox1 and Olig2 for predicted factor sites using the 15 bp affinity ...
18
Identification of binding sites in Huntingtin for the Huntingtin Interacting Proteins HIP14 and HIP14L.
... a binding site, providing evidence that these two PATs may compensate for each other in palmitoylating HTT and may compete for binding to HTT and other ...HIP14L, binding of a small HTT peptide, ...
9
A genomic analysis of disease-resistance genes encoding nucleotide binding sites in Sorghum bicolor
... Most higher plants are susceptible to infection by a variety of pathogens. A common mechanism of defense against pathogens involves a “hypersensitive response” that results in apoptosis or natural cell death of infected ...
6
Fibrinogen binding sites P336 and Y338 of clumping factor A are crucial for Staphylococcus aureus virulence.
... fibrinogen binding because the ClfAPY mutant is only partially inhibiting ...mutants. Binding of fibrinogen to ClfA could decrease opsonophagocytosis by neutrophils by reducing opsonin deposition or access ...
7
Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.
... Receptor binding is mediated by the β-hairpin (residues 19–31) of the ...pro-uPA binding to uPAR activates the adhesive and cell signaling functions of uPAR, includ- ing the interaction of uPAR with the ...
22
Studies on ATP-diphosphohydrolase nucleotide-binding sites by intrinsic fluorescence
... The binding of the nonhydro- lyzable substrate analogs decreased the fluorescence emission of both apyrases, indicating the presence of conformational changes in the neighborhood of Trp ...
5
Geometric representation and detection methods of cavities on protein surfaces
... tentative binding sites) on the surface of proteins, here called ...of binding sites [DLW08], as well as the corresponding apo and holo proteins, as the ground truth to evaluate the ...
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