Calculating a characteristic property of a molecule by correlation analysis
OwnerArtem Tcherkassov, Ridong Cheninventors
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Abstract
Methods, including computer implemented methods for calculating a characteristic property of a molecule from the 3D-structure of the molecule by correlation analysis, in which the characteristic property is equal to a contribution from the substituent parts of the molecule and a contribution from some measured property of the molecule such as the hydrophobicity and the contribution to the characteristic property from substituent parts of the molecule is equal to a function of the distance of the substituent part to a reaction center multiplied by a weight factor and substantially the same functional form of the distance function is used for calculating the contribution for each substituent part.
Claims85
A method for calculating a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the method comprising
- selecting one or more contributing substituent parts;
- for each contributing substituent part, calculating the distance from the substituent part to a reaction center;
- for each contributing substituent part, calculating a contribution of the substituent part to a characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and the where the function has a functional form that is substantially the same for all substituent parts;
- and
- calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus a contribution comprising a value of a measured property of the molecule multiplied by a weight factor.
A method for calculating a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the method comprising
- denominating one of the substituent parts as a reaction center;
- for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- for each measured property, calculating the contribution of the measured property, where the contribution is equal to the value of the measured property multiplied by a weight factor, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- calculating the property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution or contributions from the one or more measured properties.
A method for calculating a chemical characteristic property of a molecule, where the molecule has a hydrophobicity and the molecule comprises one or more substituent parts and the substituent parts are atoms contained in the molecule or groups of connected atoms contained in the molecule, the method comprising
- selecting one of the substituent parts as a reaction center;
- for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- calculating the contribution of the hydrophobicity as equal to the value of the hydrophobicity multiplied by a weight factor calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution from the hydrophobicity.
A method for calculating a chemical characteristic property of a molecule, where the molecule comprises one or more substituent parts and the chemical characteristic property is selected from the group consisting of pKa, reaction rate constants, equilibrium constants, solubility, ionization potentials, atomization energy, evaporation energy, and bond energy,
- the method comprising the steps of
- selecting one or more contributing substituent parts;
- for each contributing substituent part, calculating a distance from the substituent part to a reaction center;
- for each contributing substituent part, calculating the contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part and the function has a functional form that is substantially the same for all substituent parts;
- and
- calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule.
A system for calculating a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the system comprising:
- a processor;
- and
- a computer readable medium having computer readable program code means embodied therein for causing the system to calculate a biological characteristic property of a molecule, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one or more contributing substituent parts;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating the distance from the substituent part to a reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating a contribution of the substituent part to a characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and the where the function has a functional form that is substantially the same for all substituent parts;
- and (4) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus a contribution comprising a value of a measured property of the molecule multiplied by a weight factor.
A system for calculating a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the system comprising:
- a processor;
- and
- a computer readable medium having computer readable program code means embodied therein for causing the system to calculate a biological characteristic property of a molecule, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of denominating one of the substituent parts as a reaction center;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- (4) a computer readable program code means for causing a computer to carry out the step of, for each measured property, calculating the contribution of the measured property, where the contribution is equal to the value of the measured property multiplied by a weight factor, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- and (5) a computer readable program code means for causing a computer to carry out the step of, calculating the property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution or contributions from the one or more measured properties.
A system for calculating a chemical characteristic property of a molecule, where the molecule has a hydrophobicity and the molecule comprises one or more substituent parts and the substituent parts are atoms contained in the molecule or groups of connected atoms contained in the molecule, the system comprising:
- a processor;
- and
- a computer readable medium having computer readable program code means embodied therein for causing the system to calculate a biological characteristic property of a molecule, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one of the substituent parts as a reaction center;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- (4) a computer readable program code means for causing a computer to carry out the step of calculating the contribution of the hydrophobicity as equal to the value of the hydrophobicity multiplied by a weight factor calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- and (5) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution from the hydrophobicity.
A system for calculating a chemical characteristic property of a molecule, where the molecule comprises one or more substituent parts and the chemical characteristic property is selected from the group consisting of pKa, reaction rate constants, equilibrium constants, solubility, ionization potentials, atomization energy, evaporation energy, and bond energy, the system comprising:
- a processor;
- and
- a computer readable medium having computer readable program code means embodied therein for causing the system to calculate a biological characteristic property of a molecule, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one or more contributing substituent parts;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating a distance from the substituent part to a reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating the contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part and the function has a functional form that is substantially the same for all substituent parts;
- and (4) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule.
An article of manufacture comprising a computer useable medium having computer readable program code means embodied therein for causing a computer to calculate a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one or more contributing substituent parts;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating the distance from the substituent part to a reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating a contribution of the substituent part to a characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and the where the function has a functional form that is substantially the same for all substituent parts;
- and (4) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus a contribution comprising a value of a measured property of the molecule multiplied by a weight factor.
An article of manufacture comprising a computer useable medium having computer readable program code means embodied therein for causing a computer to calculate a characteristic property of a molecule, where the molecule has one or more measured properties and the molecule comprises one or more substituent parts, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of denominating one of the substituent parts as a reaction center;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- (4) a computer readable program code means for causing a computer to carry out the step of, for each measured property, calculating the contribution of the measured property, where the contribution is equal to the value of the measured property multiplied by a weight factor, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- and (5) a computer readable program code means for causing a computer to carry out the step of, calculating the property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution or contributions from the one or more measured properties.
An article of manufacture comprising a computer useable medium having computer readable program code means embodied therein for causing a computer to calculate a chemical characteristic property of a molecule, where the molecule has a hydrophobicity and the molecule comprises one or more substituent parts and the substituent parts are atoms contained in the molecule or groups of connected atoms contained in the molecule, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one of the substituent parts as a reaction center;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating the distance from the substituent part to the reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each substituent part other than the reaction center, calculating a contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to the inverse of the square of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part, and where the weight factor is calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- (4) a computer readable program, code means for causing a computer to carry out the step of calculating the contribution of the hydrophobicity as equal to the value of the hydrophobicity multiplied by a weight factor calculated as a regression coefficient for a multivariate regression analysis calculated for a series of molecules comprising analogs of the molecule;
- and (5) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule plus the contribution from the hydrophobicity.
An article of manufacture comprising a computer useable medium having computer readable program code means embodied therein for causing a computer to calculate a chemical characteristic property of a molecule, where the molecule comprises one or more substituent parts and the chemical characteristic property is selected from the group consisting of pKa, reaction rate constants, equilibrium constants, solubility, ionization potentials, atomization energy, evaporation energy, and bond energy, the computer readable program code means comprising:
- (1) a computer readable program code means for causing a computer to carry out the step of selecting one or more contributing substituent parts;
- (2) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating a distance from the substituent part to a reaction center;
- (3) a computer readable program code means for causing a computer to carry out the step of, for each contributing substituent part, calculating the contribution of the substituent part to the characteristic property of the molecule, where the contribution is equal to a function of the distance of the substituent part to the reaction center multiplied by a weight factor for the substituent part and the function has a functional form that is substantially the same for all substituent parts;
- and (4) a computer readable program code means for causing a computer to carry out the step of calculating the characteristic property of the molecule by summing the contributions from the contributing substituent parts of the molecule.
Dependencies are inferred from the claim text.