Back to results
US 2004/0002052 A1Published application
Systems and methods for rapid evaluation and design of molecules for predicted biological activity
OwnerLawrence B. Hendryinventor
Life of this patent
Estimating the term…
Abstract
The computer-based systems and methods are for rapidly evaluating molecules for suspected biological activity and relative potency, and for designing molecules for desired biological activity. The systems and methods enable rapid screening of large molecular databases using one or more search engines designed to identify molecules predicted to possess specific biological activities.
Claims38
A method of creating a search engine, comprising:
- selecting a binding site within nucleic acid;
- selecting a molecule having a known biological activity that fits with the binding site;
- and
- defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) docking the molecule having the known biological activity with the binding site by evaluating electrostatic interactions between the molecule and the binding site within the nucleic acid, the electrostatic interactions defining a spatial;
- (2) defining an included volume based on surfaces of the molecule that fit within the nucleic acid binding site;
- and
- (3) defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- the search engine for using at least one of the spatial, the included volume, or the excluded volume in evaluating a potential biological activity of a molecule having an unknown biological activity.
6 more elements
A method of using a search engine to evaluate a potential biological activity of a molecule having an unknown biological activity, comprising:
- selecting the search engine based on the biological activity to be evaluated, the search engine being formed by:
- (a) selecting a binding site within nucleic acid;
- (b) selecting a molecule having a known biological activity that fits with the binding site;
- and
- (c) defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) docking the molecule having the known biological activity with the binding site by evaluating electrostatic interactions between the molecule having the known biological activity and the binding site within the nucleic acid, the electrostatic interactions defining a spatial;
- (2) defining an included volume based on surfaces of the molecule having the known biological activity that fit within the nucleic acid binding site;
- and
- (3) defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- selecting the molecule having the unknown biological activity;
- and
- running the search engine using at least one of the spatial, the included volume, or the excluded volume to determine the potential biological activity of the molecule having the unknown biological activity.
9 more elements
A system for creating a search engine, comprising:
- means for selecting a binding site within nucleic acid;
- means for selecting a molecule having a known biological activity that fits with the binding site;
- and
- means for defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) means for defining a spatial by docking the molecule having the known biological activity with the binding site to evaluate electrostatic interactions between the molecule and the binding site within the nucleic acid, the electrostatic interactions defining the spatial;
- (2) means for defining an included volume based on surfaces of the molecule that fit within the nucleic acid binding site;
- and
- (3) means for defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- the search engine for using at least one of the spatial defining means, the included volume defining means, or the excluded volume defining means in evaluating a potential biological activity of a molecule having an unknown biological activity.
6 more elements
A computer-readable medium for storing software for use in performing a method of creating a search engine, the method comprising:
- selecting a binding site within nucleic acid;
- selecting a molecule having a known biological activity that fits with the binding site;
- and
- defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) docking the molecule having the known biological activity with the binding site by evaluating electrostatic interactions between the molecule and the binding site within the nucleic acid, the electrostatic interactions defining a spatial;
- (2) defining an included volume based on surfaces of the molecule that fits within the nucleic acid binding site;
- and
- (3) defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- the search engine for using at least one of the spatial, the included volume, or the excluded volume in evaluating a potential biological activity of a molecule having an unknown biological activity.
6 more elements
A system for using a search engine to evaluate a potential biological activity of a molecule having an unknown biological activity, comprising:
- means for selecting the search engine based on the biological activity to be evaluated, the search engine being formed by:
- (a) selecting a binding site within nucleic acid;
- (b) selecting a molecule having a known biological activity that fits with the binding site;
- and
- (c) defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) docking the molecule having the known biological activity with the binding site by evaluating electrostatic interactions between the molecule having the known biological activity and the binding site within the nucleic acid, the electrostatic interactions defining a spatial;
- (2) defining an included volume based on surfaces of the molecule having the known biological activity that fit within the nucleic acid binding site;
- and
- (3) defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- means for selecting the molecule having the unknown biological activity;
- and
- means for running the search engine using at least one of the spatial, the included volume, or the excluded volume to determine the potential biological activity of the molecule having the unknown biological activity.
9 more elements
A computer-readable medium for storing software for use in performing a method of using a search engine to evaluate a potential biological activity of a molecule having an unknown biological activity, the method comprising:
- selecting the search engine based on the biological activity to be evaluated, the search engine being formed by:
- (a) selecting a binding site within nucleic acid;
- (b) selecting a molecule having a known biological activity that fits with the binding site;
- and
- (c) defining search criteria forming part of the search engine, the search criteria comprising at least one of the following:
- (1) docking the molecule having the known biological activity with the binding site by evaluating electrostatic interactions between the molecule having the known biological activity and the binding site within the nucleic acid, the electrostatic interactions defining a spatial;
- (2) defining an included volume based on surfaces of the molecule having the known biological activity that fit within the nucleic acid binding site;
- and
- (3) defining an excluded volume based on surfaces of the binding site that cannot be penetrated;
- selecting the molecule having the unknown biological activity;
- and
- running the search engine using at least one of the spatial, the included volume, or the excluded volume to determine the potential biological activity of the molecule having the unknown biological activity.
9 more elements
A method of designing a new molecule for a biological activity, comprising:
- selecting a binding site within nucleic acid;
- selecting an existing molecule having a known biological activity that fits with the binding site;
- defining a molecular skeleton formed from at least one of the following:
- (1) a spatial defined by docking the existing molecule having the known biological activity with the binding site to evaluate electrostatic interactions between the existing molecule and the binding site within the nucleic acid, the electrostatic interactions defining the spatial;
- (2) an included volume defined by surfaces of the existing molecule that fit within the nucleic acid binding site;
- and
- (3) an excluded volume defined by surfaces of the binding site that cannot be penetrated;
- selecting at least two functional groups from a plurality of functional groups;
- combining functional groups that were selected to form the new molecule;
- and
- checking if the new molecule fits along the molecular skeleton;
- wherein the new molecule has a potential for the biological activity if the new molecule fits along the molecular skeleton.
9 more elements
Dependencies are inferred from the claim text.