Methods for modeling and analysis of interface between point patterns
AssigneeCity University of Hong Kong
InventorsWeiqiang Zhou, Hong Yan
Life of this patent
Estimating the term…
Abstract
Methods, systems, and articles of manufacture are described that facilitate computation of a model of an interface between two molecules and analyzing characteristics of the interface. The complex of the two molecules can be modeled, and location of the atoms on the surface can be determined. One of the two molecules can be similarly modeled, and the location of the atoms on the surface can be determined. An interface model utilizing atoms that are located in the same place on the complex and the molecule can be calculated. Properties of the interface can be utilized to analyze the interaction between the two molecules.
Claims22
A method, comprising:
- generating, by a system comprising a processor, a first three-dimensional model of a complex, wherein the complex comprises a first molecule and a second molecule, and wherein the first-three dimensional model comprises a first alpha shape;
- identifying, by the system, a first set of atoms located on a surface of the first alpha shape, wherein the surface of the first alpha shape corresponds to at least a first portion of a first surface of the first molecule and at least a second portion of a second surface of the second molecule;
- generating, by the system, a second three-dimensional model of the first molecule, wherein the second three-dimensional model comprises a second alpha shape;
- identifying, by the system, a second set of atoms located on a surface of the second alpha shape, wherein the surface of the second alpha shape includes at least the first portion of the first surface of the first molecule;
- determining, by the system, a third set of atoms included in the second set of atoms and not included in the first set of atoms;
- and
- generating, by the system, a third three-dimensional model of a binding interface between the first molecule and the second molecule in the complex based on the second alpha shape and the third set of atoms, wherein the third three-dimensional model comprises the third set of atoms.
A non-transitory computer readable storage medium having stored thereon computer executable instructions that, in response to execution, cause a system including a processor to perform operations, the operations comprising:
- generating a first three-dimensional alpha shape corresponding to a complex comprising a first molecule and a second molecule;
- identifying a first set of atoms located on a first surface of the first three-dimensional alpha shape;
- generating a second three-dimensional alpha shape corresponding to the first molecule, wherein a portion of the first surface of the first three-dimensional alpha shape includes a first portion of a second surface of the second three-dimensional alpha shape;
- determining a second set of atoms located on a second portion of the second surface of the second three-dimensional alpha shape and not included in the first set of atoms;
- and
- generating a third three-dimensional alpha shape of a binding interface between the first molecule and the second molecule in the complex based on the second three-dimensional alpha shape and the second set of atoms, wherein the third three-dimensional alpha shape comprises the second set of atoms.
A system, comprising:
- a memory that stores computer-executable instructions;
- and
- a processor that facilitates execution of the computer-executable instructions to at least:
- create a first three-dimensional alpha shape model of a complex between a biomolecule and a protein;
- identify a first set of atoms located on a surface of the first three-dimensional alpha shape model;
- create a second three-dimensional alpha shape model of the biomolecule;
- determine a second set of atoms located on a surface of the second three-dimensional alpha shape that are not included in the first set of atoms;
- and
- generate a third three-dimensional alpha shape of a binding interface between the biomolecule and the protein within the complex based on the second set of atoms and the second three-dimensional alpha shape, wherein the third three-dimensional alpha shape model comprises the second set of atoms.
Dependencies are inferred from the claim text.