• Genome-wide Prediction, Display and Refinement of Binding Sites with I" by Sashidhar Gadiraju, Carrie A. Vyhlidal et al. (uwo.ca)
  • Delila-Genome was used to examine the accuracy of individual information contents of binding sites detected with refined matrices as a measure of the strengths of the corresponding protein-nucleic acid interactions. (uwo.ca)
  • The software can then be used to predict novel sites by rescanning the genome with the refined matrices. (uwo.ca)
  • Scans of human genome assemblies required 4-6 hours for transcription factor binding sites and 10-19 hours for splice sites, respectively, on 24- and 3-node Mosix and Beowulf clusters. (uwo.ca)
  • Individual binding sites are displayed either as high-resolution sequence walkers or in low-resolution custom tracks in the UCSC genome browser. (uwo.ca)
  • Post-genome scan tools parse binding site annotations of selected chromosome intervals and compare the results of genome scans using different weight matrices. (uwo.ca)
  • Comparisons of multiple genome scans can display binding sites that are unique to each scan and identify sites with significantly altered binding strengths. (uwo.ca)
  • Conclusions: Delila-Genome was used to scan the human genome sequence with information weight matrices of transcription factor binding sites, including PXR/RXRα, AHR and NF-κB p50/p65, and matrices for RNA binding sites including splice donor, acceptor, and SC35 recognition sites. (uwo.ca)
  • Comparisons of genome scans with the original and refined PXR/RXRα information weight matrices indicate that the refined model more accurately predicts the strengths of known binding sites and is more sensitive for detection of novel binding sites. (uwo.ca)
  • In order to help identify residues that may play a role in inhibitor binding, solvent accessibilities of amino acids that comprise the inhibitor-binding sites in the structure of HIV-1 RT complexed with a dsDNA template-primer are analyzed. (neb.com)
  • Other nucleoside analog-resistance mutations located on the periphery of the dNTP-binding site may exert their effects via altered interactions with dNTP-binding site residues. (neb.com)
  • The structure of the hydrophobic region in HIV-1 RT that binds non-nucleoside inhibitors, for example, nevirapine and TIBO, has been analyzed in the absence of bound ligand. (neb.com)
  • Revealing this complex interplay between transcription factors and binding sites remains a fundamental problem for understanding the flow of genetic information. (elsevier.com)
  • The new methods circumvent computational challenges through an applied focus on families of transcription factors with similar binding properties. (elsevier.com)
  • These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which typically leads to a large number of false positives. (frontiersin.org)
  • In LS174T cells, only the upstream binding site responded to miR 145 over e pressed e o genously, and in normal colon cells endogen ously over e pressing miR 145. (pafr-signal.com)
  • Matrices are refined by adding experimentally-defined binding sites to published binding sites. (uwo.ca)
  • Many of the latter mutations are located on the surface of the DNA-binding cleft and may lead to altered template-primer positioning or conformation, causing a distortion of the geometry of the polymerase active site and consequent discrimination between normal and altered dNTP substrates. (neb.com)
  • Reference: Locations of anti-AIDS drug binding sites and resistance mutations in the three-dimensional structure of HIV-1 reverse transcriptase. (neb.com)
  • The locations of HIV-1 RT nucleoside and non-nucleoside inhibitor-binding sites and inhibitor-resistance mutations are analyzed in the context of the three-dimensional structure of the enzyme and implications for mechanisms of drug inhibition and resistance are discussed. (neb.com)
  • While some mutations that cause resistance to nucleoside analogs, such as AZT, ddI, and ddC, are located near enough to the dNTP-binding site to directly interfere with binding of nucleoside analogs, many are located away from the dNTP-binding site and more likely confer resistance by other mechanisms. (neb.com)
  • The pocket that is present when non-nucleoside inhibitors are bound is not observed in the inhibitor-free structure of HIV-1 RT with dsDNA. (neb.com)
  • An alternative possibility is restricted mobility of the p66 thumb subdomain, which is supported by the observation that structural elements of the non-nucleoside inhibitor-binding pocket may act as a 'hinge' for the thumb. (neb.com)
  • One of the oligo probes which I am using is described as 'Universal', and it does indeed bind to yeast genomic DNA (as well as mitochondrial, I assume). (bio.net)
  • Methylation and deamination of CpGs generate p53-binding sites on a genomic scale. (frontiersin.org)
  • On the other hand, the percentage of Mn 2+ sites with at least one amino acid in the "beta strand-major binder-random coil" motif of secondary structure (77.88%) does not depend on genomic GC-content. (hindawi.com)
  • Expectedly, common peaks occur more frequently in certain genomic contexts, such as CpG-rich promoters, whereas chromatin differences characterize cell-type specific TF binding. (bibsys.no)
  • These targets are commonly predicted by searching for high-scoring binding sites in the upstream genomic regions, which typically leads to a large number of false positives. (frontiersin.org)
  • Cyclic AMP treatment of hepatoma cells leads to increased protein binding at the cyclic AMP response element (CRE) of the tyrosine aminotransferase (TAT) gene in vivo, as revealed by genomic footprinting, whereas no increase is observed at the CRE of the phosphoenolpyruvate carboxykinase (PEPCK) gene. (uni-muenchen.de)
  • NEW YORK (Reuters Health) - The antiviral drug remdesivir binds to a newly identified section of a SARS-CoV-2 enzyme that is part of the virus' replication and transcription machinery, according to a structural analysis. (medscape.com)
  • The novel capsid-binding antiviral pleconaril inhibits in vitro replication of most rhinoviruses and entero-viruses. (ebscohost.com)
  • ribosome binding, mRNA processing, and transcription termination are also signaled by these sequence motifs. (wikipedia.org)
  • KCNQ2/KCNQ3 channels are preferentially localised to the surface of axons both at the axonal initial segment and more distally, and this axonal initial segment targeting of surface KCNQ channels is mediated by these ankyrin-G binding motifs of KCNQ2 and KCNQ3 [ PMID: 16735477 ]. (ebi.ac.uk)
  • As to Zn 2+ binding 3D structural motifs, Sri Krishna et al. (hindawi.com)
  • A recent alternative has been to detect specific 3D motifs which are often associated to active sites. (sciweavers.org)
  • Beta strands near Mn 2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. (hindawi.com)
  • 1 ], there are three amino acid residues most frequently found in Mn 2+ binding sites: His, Asp, and Glu. (hindawi.com)
  • Histidine has the highest normalized frequency in binding sites, while glutamic acid has the lowest normalized frequency among those three amino acid residues [ 1 ]. (hindawi.com)
  • The identification of amino acid residues involved in DNA-binding sites is critical for understanding the mechanism of these biological activities. (mdpi.com)
  • Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site (IPR020563) The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. (ebi.ac.uk)
  • Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains gene regulation. (nih.gov)
  • Recreating the mutations that led to binding site loss confirms that these sequence changes affect gene expression in some cases. (nih.gov)
  • This process, known as autoregulation, helps to maintain a so-called "steady-state" system in which a protein positively regulates its own production by binding to a regulatory element of the mRNA for the gene coding it. (ucsd.edu)
  • Using Gene Ontology (GO) and Enrichment analysis, we were able to associate (for each of the TFs studied) the target genes of both types of binding with known biological processes. (ovid.com)
  • Thus, gene regulation resulting from transcription factor binding is likely to be a major cause of divergence between related species. (sciencemag.org)
  • 1. A transgenic mouse, whose genome comprises an indicator gene under the control of a transcriptional regulatory element, wherein said transcriptional regulatory element comprises a MEF2 binding site and said indicator gene is (a) expressed in embryonic cardiac tissue, (b) not expressed in adult cardiac tissue, and (c) expressed in adult cardiac tissue in response to hypertrophic signals. (google.com)
  • Context-dependent transcription factor (TF) binding is one reason for differences in gene expression patterns between different cellular states. (bibsys.no)
  • By integrating public expression quantitative trait locus (eQTL) data, miRNA binding site predictions, small RNA sequencing, and Argonaute crosslinking immunoprecipitation (AGO-CLIP) datasets, we identified genetic variants that can affect gene expression by modulating miRNA binding efficiency. (harvard.edu)
  • Catalase haem-binding site (IPR002226) Catalases are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects. (ebi.ac.uk)
  • Identification of the tariquidar-binding site has been the subject of intensive molecular modeling studies because it is the most potent inhibitor and corrector of P-gp. (mendeley.com)
  • The structure of the complex with dimannose determined at 1.8 A resolution revealed a different conformation of the binding site than previously observed in the NMR structure of wt CV-N. Here, we present the 1.35 A resolution structure of the complex, which traps three different binding conformations of the site and provides experimental support for a locking and gating mechanism in the nanoscale time regime observed by molecular dynamics simulations. (rcsb.org)
  • Determining molecular binding sites on human serum albumin by displacement of oleic acid. (uniprot.org)
  • A systematic molecular dynamics (MD) study of zinc binding to a peptide that mimics the structural binding site of horse liver alcohol dehydrogenase (HLADH) has been conducted. (diva-portal.org)
  • But can such ChIP-seq data predict TF binding in other cellular contexts and is it possible to distinguish context-dependent from ubiquitous TF binding? (bibsys.no)
  • We compared ChIP-seq data on TF binding for multiple TFs in two different cell types and found that on average only a third of ChIP-seq peak regions are common to both cell types. (bibsys.no)
  • Putative receptors for Aβ, their binding sites, and species selectivity. (nih.gov)
  • Over the time, hundreds of compounds from different structural classes have been demonstrated to modulate, directly activate, or inhibit GABAA receptors, and most of these compounds interact with more than one binding site at these receptors. (nih.gov)
  • Due to the high flexibility of GABAA receptors and the existence of multiple drug-binding sites, the unequivocal identification of interaction sites for individual drugs is extremely difficult. (nih.gov)
  • The opiates bind to opiate receptors that are concentrated in areas within the reward system. (drugabuse.gov)
  • Mifepristone also binds to two other receptors within the body, which could have undesirable effects. (esrf.eu)
  • We determined the structure of the CVA24v to 1.40 Ã… resolution, screened different glycans bearing Neu5Ac for CVA24v binding, and structurally characterized interactions with candidate glycan receptors. (ebscohost.com)
  • Thus, unlike, SEB, SEA requires two separate binding sites for optimal activity, which may allow it to stabilize SEA interaction with T cell receptors, as well as to activate the antigen-presenting cell by cross-linking MHC class II. (rupress.org)
  • Fumarate reductase/succinate dehydrogenase, FAD-binding site (IPR003952) In bacteria two distinct, membrane-bound, enzyme complexes are responsible for the interconversion of fumarate and succinate : fumarate reductase (Frd) is used in anaerobic growth. (ebi.ac.uk)
  • 2-oxo acid dehydrogenase, lipoyl-binding site (IPR003016) The 2-oxo acid dehydrogenase multienzyme complexes from bacterial and eukaryotic sources catalyze the oxidative decarboxylation of 2-oxo acids to the corresponding acyl-CoA. (ebi.ac.uk)
  • The weaker metal ions generally form charge-solvated (CS) complexes binding amide carbonyl oxygen, while the strongest metal ion, nickel, deprotonates the amide nitrogens, probably through iminol tautomerization, and binds to the amide nitrogens. (uva.nl)
  • He produced crystals of concanavalin A complexes with methyl-glucoside and with methyl-mannoside and participated in solving the structure of this protein binding-site for saccharides. (ebooks.com)
  • Moreover, currently no crystal structure of complexes bound with PGH2 has been reported. (sciweavers.org)
  • Francelia Bound was born, it is assumed in Sullivan Co., NY in about 1854. (jansdigs.com)
  • Chromatin remodeling, methylation, histone modification, chromosome interaction, distal enhancers, and the cooperative binding of transcription co-factors all play an important role. (bioconductor.org)
  • By means of chromatin immunoprecipitation and DNA microarray analysis, the divergence in the binding sites of the pseudohyphal regulators Ste12 and Tec1 was determined in the yeasts Saccharomyces cerevisiae , S. mikatae , and S. bayanus under pseudohyphal conditions. (sciencemag.org)
  • Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identifies genome-wide TF binding sites for one particular context-the cells used in the experiment. (bibsys.no)
  • We show that by combining signal intensity with additional data-ranging from context independent information such as binding site conservation and position weight matrix scores to context dependent chromatin structure-we can predict whether a ChIP-seq peak is likely to be present in other cellular contexts. (bibsys.no)
  • Save 10% on the Poppleton In Spring (Turtleback School & Library Binding Edition) (Scholastic Reader: Level 3) by Turtleback at Translate This Website. (translateth.is)
  • Wholesale FIT supplier Travel Bound has launched a completely revamped web site, www.booktravelbound.com, with new products such as apartments, villas and ryokan inns, private sightseeing tours and transfers, as well as new features including interactive city maps, search filters and hotel hot deals and special offers. (travelagentcentral.com)
  • First it is minimizing total file transferring time by applying a Pincer-Search algorithm of Data mining approach to discover associated distributed replicas sites to share the transferring file process. (techrepublic.com)
  • For UAE and Namibia, we drove thousands of miles across those deserts in search for specific planetary analog sites. (nasa.gov)
  • So you spot-check some Google searches, but that reveals no sign of the website in the search results. (talentzoo.com)
  • You pore through the website and find that the pages that used to bring in tons of targeted Google traffic are now missing altogether, combined with other pages, or buried so deeply in the website's architecture that the search engines no longer find them important. (talentzoo.com)
  • Intracellular consequences of Aβo binding to PrP C . PrP C and mGluR5 localize to lipid rafts (indicated in orange) in synapses. (nih.gov)
  • The rationale was that a charged residue in the drug-binding pocket would disrupt hydrophobic interaction with tariquidar and inhibit its ability to rescue processing mutants or stimulate ATPase activity. (mendeley.com)
  • The addition of rough-type LPS to SFTPA1 blocked the interaction of SFTPA1 with its binding sites and the activation of MAPK1/3 and PTGS2 by SFTPA1. (bioone.org)
  • The low capacity site formed by direct apoA-I/ABCA1 interaction functions in a regulatory role, whereas the much higher capacity site generated by apoA-I/lipid interactions functions in the assembly of nascent HDL particles. (ahajournals.org)
  • In the current study, we have addressed some of these questions by characterizing the sites to which apoA-I binds during its interaction with ABCA1-expressing cells. (ahajournals.org)
  • Cell surface binding sites activated by this interaction have been studied using engineered variants of apoA-I. Importantly, ABCA1 activity creates 2 binding sites on the cell surface for apoA-I: a low capacity site created by direct apoA-I/ABCA1 interaction and a much higher capacity site that involves apoA-I/lipid interactions. (ahajournals.org)
  • Scatchard analysis revealed an apparent equilibrium dissociation constant (Kd) of 93.0 +/- 2.23 pM, and a maximal number of binding sites (Bmax) of 831.7 +/- 18.7 fmol/mg protein (mean +/- S.D., n = 4). (biomedsearch.com)
  • The maximum number of binding sites (Bmax) for control (1250 +/- 60 fmol/mg protein) was not different from the Alzheimer group (1280 +/- 40 fmol/mg protein). (diva-portal.org)
  • Kupas, K., Ultsch, A. and Klebe, G. (2008) Large Scale Analysis of Protein-Binding Cavities Using Self-Organizing Maps and Wavelet-Based Surface Patches to Describe Functional Properties, Selectivity Discrimination, and Putative Cross-Reactivity. (scirp.org)
  • Metal ion binding to peptides: oxygen or nitrogen sites? (uva.nl)
  • Compared with solution-phase behavior, the iminol binding mode shown by Mg2+ for the smallest peptides is surprising, since this ion is considered as generally binding in a CS mode in solution. (uva.nl)
  • Platelet [3H]paroxetine binding to 5-HT uptake sites in Alzheimer's disease. (diva-portal.org)
  • Platelet serotonin (5-hydroxytryptamine, 5-HT) uptake sites were studied in a control group (n = 30) and an Alzheimer group (n = 40) using [3H]paroxetine as radioligand. (diva-portal.org)
  • Thus even though several previous studies have demonstrated marked atrophy of 5-HT containing neurites and 5-HT uptake sites in Alzheimer's disease, these findings are not found in the periphery on platelets. (diva-portal.org)
  • Bacterial mRNA are usually polycistronic and contain multiple ribosome binding sites. (wikipedia.org)
  • Ribosome recruitment in eukaryotes happens when eukaryote initiation factors elF4F and poly(A)-binding protein (PABP) recognize the 5' capped mRNA and recruit the 43S ribosome complex at that location. (wikipedia.org)
  • These data indicate that particular evolutionary patterns and distinct sequence properties on scales much larger than standard transcription factor-binding sites may play an important role in Polycomb recruitment and transcriptional regulation of key developmental genes. (pnas.org)
  • A Java application that reuires a local installation of a database that provides binding site information (eg the Public Transfac 6.0 data). (warwick.ac.uk)
  • We will see how to create prompts and validators, as well as bind data to controls in a compile-time checked manner. (codeproject.com)
  • We developed a method for estimating the positional distribution of transcription factor (TF) binding sites using ChIP-chip data, and applied it to recently published experiments on binding sites of nine TFs: OCT4, SOX2, NANOG, HNF1A, HNF4A, HNF6, FOXA2, USF1 and CREB1. (ovid.com)
  • In two-dimensional [(1)H,(13)C]heteronuclear single quantum coherence NMR spectra, seven distinct resonances were observed for the (13)C-methyl-labeled oleic acid as a result of its binding to HSA. (uniprot.org)
  • That approach would allow to have distinct address for each site and makes it harder to hack on my credentials if it gets compromised. (superuser.com)
  • Eukaryotic ribosomes are known to bind to transcripts in a mechanism unlike the one involving the 5' cap, at a sequence called the internal ribosome entry site . (wikipedia.org)
  • Coenzyme A transferase binding site (IPR004163) Coenzyme A (CoA) transferases belong to an evolutionary conserved family of enzymes catalyzing the reversible transfer of CoA from one carboxylic acid to another. (ebi.ac.uk)