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Related Concept Videos

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Networks

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

Protein Organization

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 Organization

Protein Organization

Proteomics

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

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CharProtDB: a database of experimentally characterized protein annotations.

Ramana Madupu¹, Alexander Richter, Robert J Dodson

¹J Craig Venter institute, 9704 Medical Center Drive Rockville, MD 20850, USA. rmadupu@jcvi.org

Nucleic Acids Research

|December 6, 2011

Summary

CharProtDB is a curated protein database offering direct functional assignments to aid automated annotation. It supports research by consolidating manually curated and imported protein data with detailed annotations and references.

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An Integrated Approach for Microprotein Identification and Sequence Analysis

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Area of Science:

Biochemistry and Bioinformatics
Protein Annotation and Functional Genomics

Background:

Protein function assignment is crucial for understanding biological systems.
Existing annotation methods often rely on homology, leading to potential inaccuracies.
Automated annotation pipelines require reliable, experimentally validated functional data.

Purpose of the Study:

To introduce CharProtDB, a curated database of biochemically characterized proteins.
To provide direct, experimentally supported functional assignments for proteins.
To facilitate the development and improvement of automated protein annotation systems.

Main Methods:

Manual literature curation of protein biochemical characterization data.
Integration of selected records from public protein collections with confirmed direct functional assignments.
Inclusion of controlled vocabulary terms such as Gene Ontology (GO) and Enzyme Commission (EC) numbers.

Main Results:

CharProtDB offers a valuable resource for direct protein function assignments, bypassing reliance on transitive or homology-based methods.
The database contains comprehensive annotations including gene name, symbol, GO terms, EC numbers, and TransportDB accessions.
Each annotation is traceable to its original source, ensuring data provenance and reliability.

Conclusions:

CharProtDB serves as a high-quality, curated resource for experimentally validated protein functions.
The database is designed to enhance the accuracy and reliability of automated protein annotation pipelines.
It supports the broader scientific community by providing direct functional insights into proteins.