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This process is repeated until the whole residue information is diluted across the whole TF dictionary [2].
We utilized the functional residue information to select region on DDX3X that could be employed for generation of DDX3X specific analog.
Using the functional residue information at the DDX3X ATPase site, we showed that most of these residues are under strong functional constraints and that validates their conservation pattern (Figure 3).
Functional residue information of DDX3X (Figure 2) would provide more information about the mechanism by which this helicase acts and about the selectivity that differentiates DDX3X from rest of the helicases of the family.
Moreover, AS-EAST annotates the query isoform using functional amino acid residue information (Fig. 1b).
The site and residue information for PTMs were captured for 17 proteins.
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Based on key residues information, the model of HWTX-XI was docking to fit the surface of the pocket region of KV1.1 manually for KV1.1/toxin complex construction (Methods S4).
The spin systems are then assigned to the residues of the protein using both inter-residue and intra-residue information contained in the spin systems.
Such chemical shift values are then assigned to the corresponding atoms of the protein by considering the inter- and intra-residue information that different spectra contain.
We extracted relevant per-residue information out of the protein family database Pfam-A [ 43] using the output from HMMER3 [ 44].
SEPPA [ 11] was another structure-based predictor, which produced a propensity score for a target residue by considering its adjacent residues' information.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com