US 12,755,811 B1Granted

Maintaining hierarchical representation of a protein complex

AssigneeBenchling, Inc.

InventorsHenry Marfleet Willson, Katherine Christiansen-Salameh, Hailey Motooka, Madison Fletcher, Lily Helfrich

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Abstract

Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for maintaining data of a hierarchical representation of a protein complex that includes components and automatically generating missing component data of the hierarchical representation of the protein complex. By storing format templates that define structural constraints and hierarchical relationships between components of a protein complex, the described techniques enable standardized and modular representations that reduce data redundancy and improve consistency across protein designs. By automatically generating missing component data using biological transformations, the system improves data integrity, reduces manual errors, and supports scalable protein design and production.

Claims20

Dependent claims

A bioinformatics system comprising:

one or more computers and one or more storage devices storing instructions that are operable, when executed by the one or more computers, to cause the one or more computers to perform operations comprising:
maintaining, in a relational database, a plurality of format templates, each format template defining a hierarchical representation of a protein complex, wherein each hierarchical representation of a protein complex has a plurality of component slots representing respective portions of the protein complex, wherein the database stores records for a plurality of components, each component comprising data representing a respective molecular entity that can serve as one or more portions of the protein complex, and wherein the database stores links representing parent and child relationships between components of the protein complex,
wherein each format template defines one or more structural constraints between components of the protein complex, wherein the one or more structural constraints specify connection types that must be present between components of the format template, the connection types defining a biological or chemical linkage between the components;
receiving user input specifying a component of a protein complex and a component slot of a format template;
and
populating the relational database with a record representing the component while enforcing the one or more structural constraints of the format template.

3 more elements

One or more non-transitory computer storage media storing instructions that when executed by one or more computers cause the one more computers to perform operations, the operations comprising:

maintaining, in a relational database, a plurality of format templates, each format template defining a hierarchical representation of a protein complex, wherein each hierarchical representation of a protein complex has a plurality of component slots representing respective portions of the protein complex, wherein the database stores records for a plurality of components, each component comprising data representing a respective molecular entity that can serve as one or more portions of the protein complex, and wherein the database stores links representing parent and child relationships between components of the protein complex,
wherein each format template defines one or more structural constraints between components of the protein complex, wherein the one or more structural constraints specify connection types that must be present between components of the format template, the connection types defining a biological or chemical linkage between the components;
receiving user input specifying a component of a protein complex and a component slot of a format template;
and
populating the relational database with a record representing the component while enforcing the one or more structural constraints of the format template.

2 more elements

Dependencies are inferred from the claim text.