Method and system to build optimal models of 3-dimensional molecular structures
First Claim
1. A method for modeling the three dimensional structure of a molecule by determining the lowest value of conformational potential energy of a molecule by using an algorithm to define the lowest value of the conformational potential energy as the best conformation representing the three dimensional structure of the molecule, said algorithm comprising the steps of:
- a) representing the molecule in terms of coordinates defined by torsion angles of the atoms comprising the molecule;
b) specifying the number of torsion angles, n, the range of each n torsion angle, and a step size at which the values of each torsion angle is sampled, there being a total of m steps for each torsion angle, θ
r,s,r=1 to n and s=1 to m as the input set of values for each torsion angle selected;
c) selecting a set of all possible conformations of the molecule represented by a combinatorial arrangement of Mutually Orthogonal Latin Squares (MOLS) of order N, wherein said MOLS are constructed based upon the n selected torsion angles of the molecule to provide N2 sub squares in each set of MOLS, wherein N is a prime number obtained by R/m, R being 360°
, with each MOLS sub square corresponding to one possible conformation of the molecule;
d) labeling the sub squares of the MOLS by indices (u,t), u and t being integer numbers, u=1 to N and t=1 to N, and the value of the rth torsion angle in a given sub square (u,t) being chosen from the input set of values θ
r,s as
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Abstract
The present invention relates to a method to build 3-dimensional models of molecular structures corresponding to the lowest value of the potential energy function from knowledge of their chemical structures. The system uses Mutually Orthogonal Latin Squares to search through conformational space to obtain the best conformation. The system may also be used to obtain the optimum of any function, and not only those related to biomolecular structure.
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Citations
5 Claims
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1. A method for modeling the three dimensional structure of a molecule by determining the lowest value of conformational potential energy of a molecule by using an algorithm to define the lowest value of the conformational potential energy as the best conformation representing the three dimensional structure of the molecule, said algorithm comprising the steps of:
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a) representing the molecule in terms of coordinates defined by torsion angles of the atoms comprising the molecule; b) specifying the number of torsion angles, n, the range of each n torsion angle, and a step size at which the values of each torsion angle is sampled, there being a total of m steps for each torsion angle, θ
r,s,r=1 to n and s=1 to m as the input set of values for each torsion angle selected;c) selecting a set of all possible conformations of the molecule represented by a combinatorial arrangement of Mutually Orthogonal Latin Squares (MOLS) of order N, wherein said MOLS are constructed based upon the n selected torsion angles of the molecule to provide N2 sub squares in each set of MOLS, wherein N is a prime number obtained by R/m, R being 360°
, with each MOLS sub square corresponding to one possible conformation of the molecule;d) labeling the sub squares of the MOLS by indices (u,t), u and t being integer numbers, u=1 to N and t=1 to N, and the value of the rth torsion angle in a given sub square (u,t) being chosen from the input set of values θ
r,s as - View Dependent Claims (2, 3, 4, 5)
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Specification