# US 10,482,997 B2 · Method for determining three-dimensional structures of dynamic molecules > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 10,482,997 B2 - Document ID: US10482997B2 - Status: Granted - Kind: B2 - Application number: 12/677,726 - Filed: 2008-09-03 - Published: 2010-07-29 - Granted: 2019-11-19 - Earliest claimed: 2007-09-14 - Assignees: Conformetrix Limited - Applicants: Charles Douglas Blundell; Andrew Almond - Inventors: Charles Douglas Blundell; Andrew Almond - Web page: https://patentgrep.com/patent/US10482997B2 ## CPC - G16C 20/80: Data visualisation - G16B 15/00: ICT specially adapted for analysing two-dimensional [2D] or three-dimensional [3D] molecular structures, e.g. structural or functional relations or structure alignment - G16C 20/30: Prediction of properties of chemical compounds, compositions or mixtures - G16C 10/00: Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like - G16C: COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE - G16B: BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY ## Abstract 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. ## Claims ### Claim 1 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: receiving a set of internal coordinates of the molecule, said internal coordinates comprising a predefined mean dihedral angle for each bond; then assigning a probability distribution function to each bond, the probability distribution function comprising a predefined variability of the dihedral angle for said bond with respect to said predefined mean dihedral angle, the probability distribution function independent of experimental data for the solvated molecule; and then generating an ensemble of structures by implementing the set of internal coordinates and the assigned probability distribution functions by varying said dihedral angle for each bond according to said predefined dihedral angle variability; and then analyzing the ensemble of structures as a group, wherein all of the preceding steps are performed on a computer, and wherein the predefined variability of the dihedral angle for a rotatable bond is non-zero and corresponds to the associated distribution of dihedral angles. ### Claim 2 (depends on 1) The method according to claim 1, wherein the predefined variability of the dihedral angle is zero when a bond links first and second atoms and: the first and second atoms are linked via a double covalent bond, a triple covalent bond or when the first and second atoms are incorporated into an aromatic ring structure; or one of the first and second atoms is a hydrogen atom or a halogen atom; or first and second atoms are incorporated into a three or four-membered ring structure. ### Claim 3 (depends on 1) The method according to claim 1, wherein the predefined variability of the dihedral angle is non-zero and exhibits a unimodal variability of bond angles when a bond links first and second atoms via a single covalent bond and: a. one of the first and second atoms is linked to a third atom via a double or triple covalent bond; or b. the first and second atoms are oxygen atoms. ### Claim 4 (depends on 1) The method according to claim 1, wherein the predefined variability of the dihedral angle is non-zero and exhibits a bimodal variability of bond angles when a bond links first and second atoms and: the first and second atoms are incorporated into a five or six-membered saturated alicyclic ring structure; or a. the first and second atoms are linked via a single covalent bond and one of the first and second atoms is sp3-hybridised and the other of the first and second atoms is sp2-hybridised; or b. the first and second atoms are linked via a single covalent bond and said single covalent bond is conjugated to at least one further double covalent bond in the molecule. ### Claim 5 (depends on 1) The method according to claim 1, wherein said data indicating variability of said bond comprises data indicating that the variability of the bond is non-zero and exhibits a trimodal variability of bond angles when the first and second atoms are linked via a single covalent bond and: a. both of the first and second atoms are tetravalent and sp3-hybridised; or b. one of the first and second atoms are sp3-hybridised and the other of the first and second atoms is an oxygen atom. ### Claim 6 (depends on 1) The method according to claim 1, wherein the method further comprises predicting at least one experimental parameter from said generated ensemble of three-dimensional structures of said molecule. ### Claim 7 (depends on 6) The method according to claim 6, wherein the method further comprises a comparison of said at least one predicted experimental parameter to at least one further parameter derived from at least one physical experiment. ### Claim 8 (depends on 7) The method according to claim 7, wherein the method further comprises: determining an agreement function based on said comparison; generating further data representing a further ensemble of three-dimensional structures of said molecule; predicting at least one further experimental parameter from said further generated ensemble of three-dimensional structures of said molecule; comparing said at least one further predicted experimental parameter to said at least one parameter derived from at least one physical experiment; determining a further agreement function based on said comparison of the at least one further experimental parameter to said at least one parameter derived from at least one physical experiment; and generating data indicating the ensemble having the best agreement function. ### Claim 9 (depends on 1) The method according to claim 1, wherein the method further comprises predicting at least two experimental parameters from said generated ensemble of three-dimensional structures of said molecule. ### Claim 10 (depends on 9) The method according to claim 9, wherein the method further comprises a comparison of said at least two predicted experimental parameters to at least two further parameters derived from at least two physical experiments. ### Claim 11 (depends on 10) The method according to claim 10, wherein said at least two physical experiments provide data indicative of the three-dimensional structures of said molecule sampled over different time periods or over different ranges of movement of said molecule. ### Claim 12 (depends on 1) The method according to claim 1, wherein said molecule is selected from the group consisting of an organic molecule, a peptide, a carbohydrate, an antibiotic, a nucleic acid, a lipid, a metabolite, drug molecule, a protein, hyaluronan, lisinospril and AngiotensinI. ### Claim 13 (depends on 1) A method for generating data representing an optimised ensemble of three-dimensional structures of a molecule selected from a plurality of ensembles of three-dimensional structures of said molecule, wherein each ensemble is generated according to the method according to claim 1. ### Claim 14 (depends on 1) A method for predicting NMR data using an ensemble of three-dimensional structures of a molecule generated using the method according to claim 1. ### Claim 15 (depends on 1) A method for simulating a conformation of a molecule, such as a ligand molecule when bound to its intended target by generating an ensemble of three-dimensional structures of said molecule using the method according to claim 1. ### Claim 16 (depends on 1) Use of an ensemble of three-dimensional structures of a molecule, such as a ligand molecule generated according to the method set out in claim 1 to simulate a conformation of said molecule when bound to its intended target. ### Claim 17 (depends on 1) A method for simulating a bioactive conformation of a molecule selected from the group consisting of a peptide molecule, a carbohydrate molecule and a drug molecule by generating an ensemble of three-dimensional structures of said molecule using the method according to claim 1. ### Claim 18 (depends on 1) The method according to claim 1, wherein an ensemble of three-dimensional structures of a molecule selected from the group consisting of a peptide molecule, a carbohydrate molecule and a drug molecule is generated to simulate a bioactive conformation of said molecule. ### Claim 19 (depends on 1) A method for simulating the hydrogen bond occupancy in a molecule by generating an ensemble of three-dimensional structures of said peptide molecule using the method according to claim 1. ### Claim 20 (depends on 1) Use of an ensemble of three-dimensional structures of a molecule generated according to a method set out in claim 1 to simulate the hydrogen bond occupancy of said molecule. ### Claim 21 (depends on 1) A non-transitory computer readable medium comprising executable instructions configured to cause a computer to carry out the method according to claim 1. ### Claim 22 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: receiving a set of internal coordinates of the molecule, said internal coordinates comprising a predefined mean dihedral angle for each bond; then assigning a probability distribution function to each bond, the probability distribution function comprising a predefined variability of the dihedral angle for said bond with respect to said predefined mean dihedral angle, the probability distribution function independent of experimental data for the solvated molecule; then simulating the variability of the three-dimensional structure of the molecule by implementing the set of internal coordinates and the assigned probability distribution functions by varying said dihedral angle for each bond according to said predefined dihedral angle variability; and then generating an ensemble of structures based upon said simulating; and then analyzing the ensemble of structures as a group, wherein all of the preceding steps are performed on a computer, and wherein the predefined variability of the dihedral angle for a rotatable bond is non-zero. ### Claim 23 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.