Patent ID: 8010332

Claim:
An apparatus for characterizing a multi-domain protein structure, the apparatus comprising: a memory; and at least one processor, coupled to the memory, operative to: for at least one domain, calculate a hydrophobic dipole, wherein calculating the hydrophobic dipole comprises referencing a structural feature of the at least one domain, and wherein calculating the hydrophobic dipole is carried out by a component executing on a hardware processor; calculate a score representing orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure, wherein the score indicates an effect of one or more hydrophobic amino acid residues grouping near a region of domain contact, and wherein calculating the score is carried out by a component executing on a hardware processor; use the score to determine a bias in a domain hydrophobic dipole orientation within the multi-domain protein structure, and compare the score to a score of one or more native multi-domain protein structures to determine if the multi-domain protein structure resembles one or more native protein conformations, wherein determining a bias in a domain hydrophobic orientation comprises taking into account the calculated hydrophobic dipole of the at least one domain in the multi-domain protein structure, and wherein using the score to determine a bias in a domain hydrophobic dipole orientation within the multi-domain protein structure is carried out by a component executing on a hardware processor; and output the score representing orientation of the hydrophobic dipole of the at least one domain relative to a hydrophobic dipole of one or more other domains of the multi-domain protein structure to at least one of a user and a display.