Second, we predicted sites using conservation of accessibility (Methods).
This result suggests that using conservation of accessibility gives a small improvement in predicting miRNA targets though we do not rule out that more sophisticated techniques could lead to a larger improvement.
The predictions of these tools reflect miRNA:mRNA pairing, site location, conservation, site accessibility, multiple sites and expression profile [ 72].
These probabilities are estimated using the conservation and accessibility levels of the residues in the dataset of known protein structures.
Recent studies show that combining both conservation and accessibility [ 96] can achieve better results in filtering miRNA targets.
It uses a combination of energy, conservation, and accessibility scores to rank the models that are generated by the docking algorithm(s).
Here we have presented ConQuass, a very simple MQAP based directly on the compatibility between the conservation and accessibility patterns of a given structural model.
Tuncbag et al., [ 23] established a web server Hotpoint combining conservation, solvent accessibility and statistical pairwise residue potentials to computationally predict hot spots effectively.
While PPCheck can differentiate the generated decoys into native-like and non-native-like decoys with a fairly good accuracy, the results improve dramatically when features like conservation and accessibility are included.
When considering requirements for the motif to be functional (evolutionary conservation, structural accessibility of the motif and proper cell localization of the protein), more than 130 human proteins were retrieved from the UniProt/Swiss-Prot database.
Computational studies have been done based on a Cx50 homology model to assess conservation, solvent accessibility, and 3-dimensional localization of mutated residues as well as mutation-induced changes in surface electrostatic potential, H-bonding, and steric clash.
