Protein Structure and Function: Application of Bioinformatics Methods - John Rigden 2014

Predicting protein function from surface properties
Function prediction from surface properties
Combining surface properties for function prediction

In addition to electrostatics and Structure/106.html">Hydrophobicity, other Surface Properties can also influence protein function. For example, the HotPatch program utilizes A number of other surface properties to predict protein function based on its surface characteristics (Pettit et al. 2007). In this case, protein function can be determined by comparison with Databases of Proteins with similar Functions. Eleven features (including four distinct Electrostatic Properties, three measures of concavity and roughness, and four measures of hydrophobicity and hydrophilicity) are used to describe fifteen distinct hierarchically classified protein surface properties. These define functions that include a general function (each functional surface patch possesses a specific property), which is further broken down into binding function (including protein-protein, oligomeric, DNA-RNA, carbohydrate interfaces, as well as small-molecule interfaces), Enzymatic Function (including proteases, Hydrolases, transferases, oxidoreductases, and Kinases), and small ion-binding functions (anions and cations). Furthermore, the relationships between The properties of each functional group are determined, and based on their similarity, functional patches of the protein under study can be identified. Regions that do not fit into any of the categories can be designated as having an unknown function.