2-gram composition is the fraction of dipeptides composed by two amino acids with one separating residue in between.
Figure 8 and Table 2 summarize the criteria used for separating residues into distinct exchange processes and Figure 8 further indicates what residues were subsequently used as constraints in structure calculations (see below).
This motif contains two phosphotyrosine residues separated by one residue (sequence pYIpYV where pY indicates a phosphotyrosine).
Figure 1 shows the plot of the difference between D(Cα i/Cα i +4) and D O i/O i +4) for AHs specified in the PDB files (in red, mean=0.16 Å, standard deviation (sd)= 0.34 Å), and for all residues separated by four residues but not part of a helix (in blue, mean=0.71 Å, sd=0.75 Å).
Taking this principle, CeePre2 converts the prediction results of CeePre1 into the four features at the second stage to integrate separated antigenic residues into a cluster of epitope residues, enhancing the prediction performance for many cases.
However, the result of this process was a decision not to establish separate residue limits for herbicide-tolerant cultivars.
For the majority regions of this protein, there is a good agreement between the predicted and observed RD values despite that several separate residue positions such as 6, 61, 91, 132 and 134 are poorly predicted (blue), as can be seen from Figure 7A.
The nitroxide radical tag was covalently attached at the 5′-terminus of the TAR as a separate residue and subsequently minimized.
CeePre2 again demonstrates the clustering effect on this antigen: separated antigenic residues are aggregated into epitopes, while isolated epitope and non-epitope residue predictions by CeePre1 are removed by the second stage of CeePre2.
Amino acids Q139, P140, and D141 form the tip of the loop and are separated from residues R145 and S146 by three intervening amino acids.
