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US 8,078,432 B2Granted
Binding evaluation method for macromolecular compound
AssigneeIshikawajima-Harima Heavy Industries Co., Ltd.
InventorsHaruki Eguchi, Toshikazu Yano
Life of this patent
Estimating the term…
Abstract
A method for evaluating the binding of an evaluation target molecule with respect to a macromolecular compound based on numerical calculations and which detects the binding sites of the evaluation target molecule with respect to the macromolecular compound as a site where electronic states in a predetermined restricted region including the evaluation target molecule and the part of the macromolecular compound, which is adjacent to the evaluation target molecule, are unstable.
Claims29
A binding evaluation method comprising:
- a step S1 of detecting a binding position of an evaluation target molecule in which internal energy, calculated using a classical molecular dynamics method, of a targeted model for analysis formed from a macromolecular compound and the evaluation target molecule takes on a minimum value as a binding position with respect to an active site, as a preprocess;
- a step S2 of setting each of initial values of a wave function Φ(r) and an effective potential V(r) regarding a restricted region (G);
- a step S3 of calculating the initial values of charge density ρ(r) based on all electrons in the restricted region (G) by assigning the initial values of wave function Φ(r) to a formula (1):
- ρ(r)=ΣΦ*(r)Φ(r) (1);
- a step S4 of calculating the wave function Φ(r) in the restricted region (G) by solving a Schrödinger wave equation (2):
- [
- -
- 1
- 2
-
- ∇
- 2
-
- +
- V
-
- {
- r
- ,
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-
- Φ
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- based on the initial values of the effective potential V(r) and those of charge density ρ(r);
- a step S5 of determining the charge density ρ(r) by assigning the wave function Φ(r) derived from the Schrödinger wave equation (2) to the formula (1);
- a step of S6 of determining whether or not the charge density ρ(r) equals the charge density ρ(r) derived in the previous calculation and determining the charge density ρ(r) which satisfies the Schrödinger wave equation (2) and equals the previous charge density ρ(r) by repeatedly solving the Schrödinger wave equation (2) until the charge density ρ(r) currently determined equals the charge density ρ(r) previously determined;
- a step S7 of calculating LUMOf+(r) and HOMOf−(r) as values of Fukui functions (3) and (4):
- f
- +
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- r
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- =
- 1
- Δ
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- ρ
- N
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- (
- 3
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- in the restricted region (G) by assigning the charge density ρ(r) to Fukui functions (3) and (4);
- a step S8 of displaying the LUMOf+(r) and the HOMOf−(r) by images;
- and
- a step S9 of identifying a binding site between the evaluation target molecule and the macromolecular compound, wherein the steps S1 to S9 are based on at least numerical calculations using a computer.
116 more elements
A binding evaluation method comprising:
- detecting a binding position of an evaluation target molecule with respect to an active site of an a macromolecular compound, in which internal energy takes on a minimum value, using a classical molecular dynamics method, calculated using a targeted model formed based on the macromolecular compound and the evaluation target molecule;
- setting initial values of a wave function Φ(r) and an effective potential V(r) regarding a restricted region (G) with respect to the detected binding position;
- calculating the initial values of a charge density ρ(r) based on all electrons in the restricted region (G), by assigning the initial values of wave function Φ(r);
- calculating the wave function Φ(r) in the restricted region (G) by solving a Schrödinger wave equation;
- based on the initial values of the effective potential V(r) and the charge density ρ(r);
- iteratively updating the charge density ρ(r) by assigning the wave function Φ(r) derived from the Schrödinger wave equation, until convergence;
- calculating a values of a plurality of Fukui functions in the restricted region (G) by assigning the charge density ρ(r) to the plurality of Fukui functions;
- and
- identifying a binding site of the evaluation target molecule at the macromolecular compound, wherein at least the iteratively updating are based on at least numerical calculations using a computer.
6 more elements
Dependencies are inferred from the claim text.