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The major histocompatibility complex (MHC) binding motif can be determined by binding or functional assays using analogs of the minimal active sequence.
The reviewed findings provide a proof of principle that targeting of critical repetitive sequences (not necessarily coding regions), which allow for clustering of drug binding motif, can be the paradigm for region specificity of small molecular weight agents.
The conserved NFκB binding motif can be found three times within the human SIRT1 promoter sequence.
Indeed a Tcf/LEF binding motif can be found within the promoter region of Hunk.
Typically, the HSP72 binding motif can be defined by a linear sequence of 7 amino acids containing hydrophobic side groups or aromatic rings (1).
Conservation of the binding motif can be assessed through comparative genomics analyses, which can also be used to validate robust multispecies scoring matrices that are well suited for metagenomic analyses (Cornish et al., 2012).
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The most prominent role is played by the interactions between the DNA bases, where two binding motifs can be recognized: planar hydrogen bonding and vertical stacking.
These binding motifs can be used to identify potential MHC-binding peptides from a given protein.
Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms.
Over 90% of the sites identified can be validated by ChIP-qPCR, and de novo consensus binding motifs can be predicted from the overlapping regions [ 31].
The analysis indicates that some interesting binding motifs can be found, such as neural-specific Elavl2, cytokine's degrading Zfp36, and mRNA trafficking Khsrp.
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