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Short binding motifs, however, may bind too weak, because they primarily rely on hydrophobic interactions [56], [60].
Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions.
There are two major classes of MHC molecules: MHC class I (MHC-I) molecules characterized by short binding peptides, usually consisting of nine residues; and MHC class II (MHC-II) molecules with binding peptides that range from 11 to 30 residues in length, although shorter and longer peptide lengths are not uncommon [2].
Chicz et al. (1993) suggest that the self peptides have a physiological role in modulating the immune response [10]: Since overstimulation by antigen can induce peripheral tolerance, the self ligands may serve not only to prevent antigenic peptides with short binding half-lives from binding, but also prevent over-presentation of foreign antigen in vivo.
These short binding site sequences are often referred to as sequence motifs and occur in recurring patterns across DNA [ 2].
MEME is complemented by DREME (Bailey, 2011), which uses a simpler, non-probabilistic model (regular expressions) to describe the short binding motifs characteristic of single eukaryotic TFs.
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But unlike its cousin sport of wakeboarding — which is an amalgam of surfing and snowboarding that uses short, binding-equipped boards — wakesurfing avoids towropes once a rider is standing, relying instead on the hydrodynamics of an artificially created wave.
It was found that H2CO molecule adsorption on h-AlN nanosheet had relatively higher adsorption energy and shorter binding distance and finally much more reactive in the adsorption of H2CO compared with the h-SiC and graphene sheets.
Our calculated results showed that Ni-SWCNTs had much higher adsorption energy, larger net charge transfer values and shorter binding distances than pure SWCNTs owning to chemisorption of the SO2 molecule.
However, in shorter binding sites exhibiting weaker conservation, BigFoot outperforms the single-alignment method.
Deuterium bonds can exhibit a higher binding energy and a shorter binding length than protium (hydrogen) bonds.
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