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US 9,002,658 B2Granted
Identifying components of a network having high importance for network integrity
AssigneeE-Therapeutics PLC
InventorsMalcolm P. Young, Peter E. Andras, Mark A. O'Neill
Life of this patent
Estimating the term…
Abstract
A computer system (2) is provided which is arranged to receive network data (1) identifying nodes and links between nodes. The computer system (2) processes the input network data (1) to utilise the network topology to identify nodes and links having high importance for network integrity. A report (4) identify the critical components can then be output.
Claims25
A computer implemented method of identifying target proteins for drug therapies comprising:
- obtaining proteome data defining proteins and proteins interactions for an organism to be targeted;
- storing the proteome data in a computer in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- and
- utilizing the computer to implement the method of:
- assigning each of the plurality of nodes to clusters thereby dividing the nodes into a number of clusters of nodes;
- calculating a cost value for the assignment that is indicative of the extent to which nodes directly connected to each other by links are assigned to a same cluster among the number of clusters and nodes not directly connected to each other by links are assigned to a different cluster among the number of clusters;
- iteratively modifying the assignment of the nodes to the number of clusters using the determined cost values to determine an assignment of the nodes to the number of clusters for which a cost value for the assignment is indicative of an assignment of the nodes in which the nodes directly connected to each other by links are assigned to a same cluster among the number of clusters and nodes which are not directly connected to each other by links are assigned to a different cluster among the number of clusters;
- and
- synthesizing therapeutic drugs, based on identifying as identified target proteins, proteins associated with those of the nodes that are connected by the links wherein the nodes are assigned to different clusters.
6 more elements
A method of manufacturing a therapeutic drug comprising:
- using a computer to identify a potential pharmaceutical compound by:
- obtaining proteome data defining proteins and proteins interactions for an organism to be targeted;
- storing the proteome in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- assigning each of the plurality of nodes to clusters thereby dividing the nodes into a number of clusters of nodes;
- calculating a cost value indicative of the extent to which nodes directly connected to each other by links are assigned to a same cluster among the number of clusters and nodes not directly connected to each other by links are assigned to a different cluster among the number of clusters;
- iteratively modifying the assignment of the nodes to the number of clusters using the determined cost values to determine an assignment of the nodes to the number of clusters for which a cost value for the assignment is indicative of an assignment of the nodes in which the nodes directly connected to each other by links are assigned to a same cluster among the number of clusters and nodes not directly connected to each other by links are assigned to a different cluster among the number of clusters;
- and
- identifying as target proteins, proteins associated with those of the nodes that are connected by the links wherein the nodes are assigned to different clusters;
- identifying one or more compounds which react with one or more of the identified target proteins;
- and
- manufacturing a therapeutic drug containing compounds identified as reacting with an identified target protein among the identified target proteins.
8 more elements
A computer implemented method of identifying target proteins for drug therapies comprising:
- obtaining proteome data for an organism to be targeted;
- and
- utilizing the computer to implement the method of:
- representing the proteome data in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the network data to determine for each node in the network, the number of links associated with each node;
- identifying as hub nodes, nodes in the network which are associated with more than a threshold number of links;
- and
- synthesizing therapeutic drugs, based on identified target proteins associated with the identified hub nodes.
5 more elements
A computer implemented method of identifying target proteins for drug therapies comprising:
- obtaining proteome data for a host organism and an organism to be targeted;
- and
- utilizing the computer to implement the method of:
- representing the proteome data for the host organism in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the network data for the host organism to determine for each node in the network the number of links associated with each node;
- identifying as hub nodes in the network defined by the network data for the host organism, nodes which are associated with more than a threshold number of links;
- representing the proteome data for the organism to be targeted in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the network data for the target organism to determine for each node in the network defined by the network data the number of links associated with each node;
- identifying as hub nodes in the network defined by the network data for the target organism, nodes which are associated with more than a threshold number of links;
- and
- synthesizing therapeutic drugs, based on identified target proteins associated with the identified hub nodes in the proteome of the target organism which are not hub nodes in the proteome of the host organism.
8 more elements
A method of manufacturing a therapeutic drug comprising:
- using a computer to identify a potential pharmaceutical compound by:
- obtaining proteome data for an organism to be targeted;
- representing the proteome in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the network data to determine for each node in the network the number of links associated with each node;
- identifying as hub nodes, nodes in the network which are associated with more than a threshold number of links;
- identifying as target proteins for targeting by drug therapies, proteins associated with the identified hub nodes;
- and
- identifying one or more compounds which react with the identified target proteins;
- and
- manufacturing a therapeutic drug containing compounds identified as reacting with the identified target proteins.
7 more elements
A non-transient computer readable medium storing computer interpretable instructions which when interpreted by a programmable computer cause the computer to:
- store proteome or an organism to be targeted in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- process the stored network data to determine for each node in the network defined by the stored network data the number of links associated with each node;
- identify as hub nodes, nodes in the network defined by the stored network data which are associated with more than a threshold number of links;
- and
- synthesize therapeutic drugs, based on identified target proteins associated with the identified hub nodes.
2 more elements
An information processing apparatus for identifying target proteins for targeting by drug therapies comprising:
- a data store configured to store proteome data for an organism to be targeted as network data defining a plurality of nodes and a plurality of links between the nodes wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- a processing unit operable to process network data stored in the data store to determine for each of the nodes of the network defined by the stored network data, the number of links associated with each node and identify as hub nodes, nodes in the network which are associated with more than a threshold number of links;
- an output unit operable to output data identifying one or more target proteins for targeting by drug therapies proteins corresponding to the identified hub nodes;
- and
- synthesizing therapeutic drugs based on the output data.
2 more elements
A computer implemented method of identifying target proteins for drug therapies comprising:
- obtaining proteome data defining proteins and proteins interactions for an organism to be targeted;
- storing the proteome data in a computer in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the stored network data using the computer to:
- determine from the nodes a set of nodes that are of importance for the structural integrity of the network defined by the stored network data, wherein the set of nodes comprises nodes selected from any of:
- hub nodes in the network;
- nodes in the network that are difficult to route around;
- and
- nodes in the network involved in links between sub-networks of interconnected nodes which have more links to other nodes in the sub-network than other nodes in the rest of the network;
- identify nodes of the network associated with links to nodes determined to be in the set of nodes of importance for the structural integrity of the network;
- outputting data as data identifying target proteins, data identifying proteins corresponding to the nodes of the network associated with links to nodes determined to be in the set of nodes of importance for the structural integrity of the network;
- and
- synthesizing therapeutic drugs based on the output data.
9 more elements
A method of manufacturing a therapeutic drug comprising:
- using a computer to identify a potential pharmaceutical compound by:
- obtaining proteome data defining proteins and proteins interactions for an organism to be targeted;
- storing the proteome data in the form of network data defining a plurality of nodes and a plurality of links between the nodes, wherein the nodes are associated with proteins and the links are indicative of protein interactions;
- processing the stored network data to:
- determine from the plurality of nodes a set of nodes of importance for the structural integrity of the network defined by the stored network data, wherein the set of nodes comprises nodes selected from any of:
- hub nodes in the network;
- nodes in the network that are difficult to route around;
- and
- nodes in the network involved in links between sub-networks of interconnected nodes which have more links to other nodes in the sub-network than other nodes in the rest of the network;
- identify nodes of the network associated with links to nodes determined to be in the set of nodes of importance for the structural integrity of the network;
- and
- outputting data as data identifying target proteins, data identifying proteins corresponding to the nodes of the network associated with links to nodes determined to be in the set of nodes of importance for the structural integrity of the network;
- and
- identifying one or more compounds which react with one or more of the identified target proteins;
- and
- manufacturing a therapeutic drug containing compounds identified as reacting with an identified target protein.
13 more elements
Dependencies are inferred from the claim text.