The cap moiety occupies the GTP binding pocket while the remaining of the RNA chain makes minimal interactions with the protein and appears stabilized by intra-molecular interactions as described in the next section.
Of these, 56 sites which had scores significantly beyond the threshold of -1 set by the algorithm were identified as candidate CAP binding sites while the remaining 6 sites, which were separated in energy from the rest of the sites by a significant gap, and which all scored below the threshold, were considered to have been selected due to non-specific binding and discarded.
A3A, A3C, and A3H present one copy of the zinc-binding domain, while the remaining harbor two copies; the N- and C-terminal domains are named CD1 and CD2, respectively.
In the case of the HA protein, 5 of the 8 consensus epitopes were located in the globular zone, very close to the sialic acid-binding site, while the remaining epitopes were located in the stem region.
However, 121 encoded proteins in the 'other binding' category could bind to zinc ion, while the remaining proteins had various ion binding functions.
In this case, MEL1 has one binding site for Gal4p, while the remaining seven GAL genes, including GAL1 and GAL2, have two binding sites.
Regarding molecular function in the GO resource, defined as 'what a gene product does at the biochemical level', we found that 71% of the ESTs were dedicated to binding and catalytic functions, while the remaining ESTs were mostly dedicated to structural molecule activity (8%) and transporter activity (6%).
We then assessed the binding of the remaining 49 hCXCL1 mutants to soluble SA129, SA138, and SA157*.
At that concentration, 8 aptamers display up to five-fold increase of binding to U87MG cells with respect to the starting pool, while the remaining 13 aptamers show no specific binding to U87MG (not shown).
For each grid the probabilities are calculated via the formulation given below by Eqs. 1, 2, 3, and 4. For the 1st grid 20 binding energies are available, while for the remaining grid pairs 400 binding energies are available; the corresponding statistical weight matrix is given in Eq.1 and 2, respectively.
