1. A computer-implemented method of characterizing an engineered multi-domain protein structure, comprising executing, via a computer, the following steps: for at least one domain, calculating 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; calculating 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 engineered 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; using the score to determine a bias in a domain hydrophobic dipole orientation within the multi-domain protein structure, and compare the score of the engineered multi-domain protein structure to a score of one or more native multi-domain protein structures to determine if the engineered 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 outputting 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.