For this analysis, odorant binding proteins are defined as the 49 VectorBase genes annotated with InterPro domain IPR006625 (Insect pheromone/odorant binding protein PhBP).
One group of RNA binding proteins is defined by the presence of a CCCH type zinc finger motif that directly binds to RNA.
DNA/RNA-binding proteins were defined as those proteins whose annotations included the following keywords in Swiss-Prot, TrEMBL, and GOA annotations: DNA, RNA, ribosome al), RNP, ribonucleo-, helicase, nuclease, or nucleic acid binding.
The binding sites of the COX-1 (3KK6) and hERG proteins were defined with the radii of 6.988 and 7.411 Ǻ respectively.
Snx proteins are defined by the presence of a phospholipid binding (PX) domain (Figure 3B) [30], [30].
MYB proteins are defined by a highly conserved MYB DNA-binding domain at the N-terminus [ 3].
Briefly, the binding site of the protein is defined based on its known active ligand with a minimum of 3 Å to any ligand heavy atom.
Furthermore, conformation of the integrin-binding loop in a protein is defined not only by physicochemical properties and conformation of the sequence itself, but also by its structural environment and therefore of the potential biological activity.
In a protein-DNA complex, an amino acid residue in the protein is defined as DNA-binding site if the distance between any atoms of this residue and any atoms of the DNA molecule is less than a distance threshold.
Among these RNA binding proteins are the historically defined heterogenous nuclear ribonucleoproteins (hnRNPs) which mediate multiple steps in the mRNA lifecycle such as processing, nuclear export, and delivery to the cytoplasm [7], [8].
We have recently reported the design and validation of a series of new peptide aptamer scaffolds, culminating in Stefin A quadruple mutant Tracy (SQT), derived from the mammalian protease inhibitor Stefin A. Peptide aptamers represent a relatively new class of alternative binding proteins, and are defined as binding peptides constrained within a protein scaffold.
