Residue depth has also been utilized in predicting small molecule binding site on proteins, with accuracy statistically on par with other conventional methods.
[6] More recently, Song et al. described another sequence-based method that also uses support vector regression to quantify the RD-sequence relationship.
[7] Their webserver Prodepth, is developed to facilitate RD prediction analysis for sequences submitted by interested users.
In addition, Prodepth server can predict the solvent-accessible surface area (ASA) value for each residue for users' submitted sequence.
[8] The pKa equation is a linear combination of a few features, including: depth, number of hydrogen bond, electrostatic energy, solvent accessible surface area.