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The basic binding segment for PEG was found to be close to an averaged molecular weight of ∼4000 Da.
For the binding of DA, Tyrosine (Tyr10) was identified as the strong binding site, and serine-asparagine-lysing (SNK 26 28)) segment was the weak binding segment.
The key differences between CompA and other members of the actin fold family are: (i) the presence of a cluster binding segment, the "cluster helix"; (ii) the [4Fe-4S] cluster; and (iii) the location of the homodimer interface, which involves the bridging cluster.
We examine two possibilities: (1) exactly one binding segment is always present or (2) either one or two binding segments are present in each binding peptide.
Therefore, all GA-sequences should, their overall individuality [1] notwithstanding, contain or be flanked by a common binding segment for these universal linker molecules.
The second domain, NBD94566 663, covering the amino acids close to the nucleotide binding segment NBD94444 547, has been crystallized by vapor diffusion using 2-methyl-2,4 pentanediol as a precipitant in a form suitable for X-ray diffraction analysis.
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263 of the 442 high confidence HSF binding sites found in that study coincided with HSF binding segments we found (Table S2).
Most importantly, the proposed methods can make principled probabilistic inference from multiple evidence sources, such as, multiple statistical models (motifs) of the TFs, evolutionary conservation, regulatory potential, CpG islands, nucleosome positioning, DNase hypersensitive sites, ChIP-chip binding segments and other (prior) sequence-based biological knowledge.
Discontinuous binding segments are aligned to a candidate protein and the value of root mean square deviation (RMSD) between all binding segments and a candidate protein is calculated.
The residues identified as binding sites have been studied in terms of binding segments.
We then identified the binding segments in the interface of the query complex.
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