Abstract: A method and system to identify an epitope unique to a misfolded form of a protein is provided. Sets of one or more amino acid residues are selected from a model representing the structure of the protein; the free energy of unfolding of each set is determined; and the epitope is identified from the sets having a total probability of unfolding above a minimum probability or a free energy of unfolding below a minimum energy. In other aspects, the invention provides for the use of epitopes identified by the epitope prediction methods, and related antibodies, to diagnose and treat disease and to screen samples for the presence of such epitopes.

Abstract: A method and system to identify an epitope unique to a misfolded form of a protein is provided. Sets of one or more amino acid residues are selected from a model representing the structure of the protein; the free energy of unfolding of each set is determined; and the epitope is identified from the sets having a total probability of unfolding above a minimum probability or a free energy of unfolding below a minimum energy. In other aspects, the invention provides for the use of epitopes identified by the epitope prediction methods, and related antibodies, to diagnose and treat disease and to screen samples for the presence of such epitopes.

Abstract: The present disclosure describes methods, systems and techniques for determining a localized dielectric property of a molecule. A molecular model of at least a portion of the molecule is obtained. The molecular model is partitioned into cavities, and for each of the cavities, the permittivity within the cavity is iteratively determined based on permittivity outside of the cavity and electronic and nuclear polarizability within the cavity. Beneficially, this allows for different permittivities to be determined for different portions of the molecule, and is advantageous over simply assigning a single permittivity to the entire molecule.

Abstract: A method and system to identify an epitope unique to a misfolded form of a protein is provided. Sets of one or more amino acid residues are selected from a model representing the structure of the protein; the free energy of unfolding of each set is determined; and the epitope is identified from the sets having a total probability of unfolding above a minimum probability or a free energy of unfolding below a minimum energy. In other aspects, the invention provides for the use of epitopes identified by the epitope prediction methods, and related antibodies, to diagnose and treat disease and to screen samples for the presence of such epitopes.