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Sequence component (Sc): List of residues forming a 3D pattern.
The residue sequence is also available to search biomolecules based on an ordered list of residues.
A new layer starts whenever there is a change in the list of residues lining the tunnel along its length.
The output of metaPPI is also a continuous patch, rather than a list of residues such as provided by CPORT and the other individual predictors.
A complete list of residues that remained in contact with the substrate as it moved from the S1 site towards the extracellular side was prepared for DAT.
Our study puts forward a list of residues important for DHA1, drug-proton antiporters, when compared against SP, a symporter family.
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In any case, ABS-Scan analysis has been successfully performed on 54 (the remaining 25 cases were not processed by default steps due to unusual atom types in proteins/ligands) complexes, which provide the extent of contribution to ligand binding of each residue in each site, in the form of a ranked list of residue-wide ∆∆G values.
A more comprehensive listing of residues that undergo significant chemical shift changes is shown in Fig. 3D.
The details of the dataset and the ranked lists of residues in the order of their contribution to ligand binding identified for all the complexes is made available to the community - http://proline.biochem.iisc.ernet.in/abscan/validation.in/abscan/validation
Fourth, we marked the residues that both were on the list of ten residues that appear most frequently in unstructured protein regions and were determined to have codon usage rates less that the selected reference level.
By using these analyses, for each Pfam domain, the pipeline provided a list of position-residue type relevant residues, which could thus be mapped to all Cp ORFs with assigned Pfam domain.
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Justyna Jupowicz-Kozak
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