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US 10,482,997 B2Granted
Method for determining three-dimensional structures of dynamic molecules
AssigneeConformetrix Limited
InventorsCharles Douglas Blundell, Andrew Almond
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AssigneeConformetrix Limited
InventorsCharles Douglas Blundell, Andrew Almond
Estimating the term…
The present invention relates to a method for determining three-dimensional structures of molecules, particularly, but not exclusively, dynamic organic molecules of biological interest such as peptides, carbohydrates, proteins and drug molecules. A first aspect of the present invention provides a method for generating data representing an ensemble of three-dimensional structures of a molecule, the molecule comprising first and second atoms linked by at least one bond, said bond having an associated angle, and the angle varying to generate a plurality of three-dimensional structures of said molecule, the method comprising: receiving data representing said molecule, said data comprising data indicating variability of said angle; and generating an ensemble of structures such that the angle has an associated value selected based upon said variability. A second aspect of the present invention provides a computer implemented method for simulating the variability of the three-dimensional structure of a molecule.
A method for generating an ensemble of discrete molecular structures representing a range of three-dimensional shapes of a solvated molecule, the molecule comprising a plurality of bonds each having an associated mean dihedral angle, wherein at least one bond is a rotatable bond having an associated distribution of dihedral angles, the method comprising:
A method for simulating the variability of the three-dimensional structure of a molecule, the molecule comprising a plurality of bonds each having an associated mean dihedral angle, wherein at least one bond is a rotatable bond having an associated distribution of dihedral angles, the method comprising:
A non-transitory computer readable medium comprising executable instructions usable to generate an ensemble of three-dimensional structures of a molecule and to analyze the ensemble of three-dimensional structures of the molecule as a group, the molecule comprising a plurality of bonds, wherein at least one bond is a rotatable bond having an associated distribution of dihedral angles, the medium comprising a set of internal coordinates of the molecule, said internal coordinates comprising a predefined mean dihedral angle for each bond, and a probability distribution function for each bond, said probability distribution function comprising a predefined variability of the dihedral angle for said bond with respect to said predefined mean dihedral angle, wherein the predefined variability of the dihedral angle for a rotatable bond is non-zero and corresponds to the associated distribution of dihedral angles and wherein the probability distribution function independent of experimental data for the solvated molecule.
Dependencies are inferred from the claim text.