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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 Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Protein Families

Protein Families

Protein families are groups of homologous proteins; that is, they have similarities in amino acid sequences and three-dimensional structures. Protein families usually occur because of gene duplication, where an additional copy of a gene is inserted into the genome of an organism. Mutations that change the amino acids but still allow the protein to be properly synthesized, will lead to new protein family members. If these new proteins contain similar amino acids in key locations, protein...

Genome Annotation and Assembly

Genome Annotation and Assembly

The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.

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.

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Related Experiment Video

Updated: Jun 25, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Is protein classification necessary? Toward alternative approaches to function annotation.

Donald Petrey¹, Barry Honig

¹Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Columbia University, New York, NY 10032, USA.

Current Opinion in Structural Biology

|March 10, 2009

Summary

This summary is machine-generated.

Protein classification for function annotation is challenging due to multifunctionality. Strategies avoiding classification may offer a more robust approach to understanding protein function.

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Last Updated: Jun 25, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Creating and Applying a Reference to Facilitate the Discussion and Classification of Proteins in a Diverse Group

Published on: August 16, 2017

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

The exponential growth of protein sequence databases presents significant challenges for accurate function annotation.
Current methods often rely on classifying proteins into sequence and structural groups to simplify annotation.

Purpose of the Study:

To evaluate the effectiveness of protein classification strategies for function annotation.
To propose alternative approaches for robust protein function assignment.

Main Methods:

Analysis of protein sequence and structural data.
Examination of multifunctionality and structural diversity within protein families.
Critique of classification-based annotation methods.

Main Results:

Closely related proteins exhibit significant multifunctionality and structural diversity.
Overall sequence or structural similarity can be misleading for function assignment.
Classification strategies often confound efforts to accurately annotate protein function.

Conclusions:

Protein classification is an inadequate strategy for comprehensive function annotation.
Alternative, non-classification-based approaches are needed for robust protein function assignment.
Future research should focus on methods that account for protein multifunctionality and structural plasticity.