Computational method for predicting functional sites of biological molecules

A non-transitory computer readable medium comprising instructions for generating prediction models for prediction of biomolecule-to-biomolecule interaction sites, the instructions, when executed by at least one processor, comprising functionality to:

• receive training data including data representative of a plurality of biomolecules having known biomolecule-to-biomolecule interaction sites;
• for each biomolecule of the plurality of biomolecules
• generate a plurality of three dimensional probability density maps, each three dimensional probability density map representing a probability of a non-covalent interacting atom on a surface of the biomolecule interacting with a corresponding atom type of a plurality of atom types;
• for each surface atom of a plurality of surface atoms of the biomolecule, calculate a plurality of attributes, each attribute associated with a different one of the plurality of atom types;
• train a prediction model for each of the atom types of the plurality of atom types based on the attributes calculated for each biomolecule of the plurality of biomolecules.

A non-transitory computer readable medium comprising instructions for determining clusters of amino acid conformations, the instructions, when executed by at least one processor, comprising functionality to:

• for each protein of a plurality of proteins in a protein database:
• for each amino acid type of a plurality of amino acid types:
• determine data characterizing a conformation of each instance of the amino acid type in the protein including determining a vector of torsion angle elements for each instance of the amino acid type in the protein;
• and
• process the data characterizing the conformation determined for each instance of each type of amino acid for each protein in the protein database to identify clusters of amino acid instances having similar conformation characteristics.