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Related Concept Videos

Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Protein Organization01:24

Protein Organization

Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
Protein Organization01:13

Protein Organization

Overview
Conservation of Protein Domains02:26

Conservation of Protein Domains

Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
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Published on: July 16, 2017

A domain specific data management architecture for protein structure data.

Yanchao Wang1, R Sunderraman, Hao Tian

  • 1Dept. of Comput. Sci., Georgia State Univ., GA 30303, USA.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|October 20, 2007
PubMed
Summary
This summary is machine-generated.

We introduce a novel database architecture for managing protein structure data, enhancing object-oriented database systems with specialized layers for easier data querying and integrity. This system simplifies complex biological data requests for scientists.

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Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
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Area of Science:

  • Bioinformatics
  • Database Management
  • Structural Biology

Background:

  • Managing complex protein structure data requires specialized database solutions.
  • Existing Object-Oriented Database (OODB) systems lack domain-specific features for biological data.
  • Efficient querying and data integrity are crucial for protein structure analysis.

Purpose of the Study:

  • To propose an extended OODB architecture for managing protein structure data.
  • To introduce domain-specific layers, Protein-QL and Protein-OODB, for enhanced data management.
  • To lay the groundwork for a general Biological Object-Oriented Database Management System (Bio-OODBMS).

Main Methods:

  • Extending OODB architecture with Protein-QL (query language) and Protein-OODB (data layer).
  • Defining three internal data types for primary, secondary, and tertiary protein structures.
  • Implementing Protein-QL queries using lambda-DB, compiling them into OQL.
  • Introducing constraints to ensure protein data integrity.

Main Results:

  • A novel architecture for protein structure data management is proposed.
  • Protein-QL simplifies data requests for domain scientists.
  • The system supports efficient querying and ensures data integrity.
  • The architecture serves as a foundation for a broader Bio-OODBMS.

Conclusions:

  • The proposed architecture effectively manages protein structure data within an OODB framework.
  • Domain-specific layers enhance usability and data integrity for biological applications.
  • This work represents a significant step towards a general Bio-OODBMS.