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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...

Protein Families

Protein Families

Conservation of Protein Domains Over Different Proteins

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...

Conservation of Protein Domains

Conservation of Protein Domains

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.

Conserved Binding Sites

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...

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Updated: Apr 1, 2026

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

Protein function annotation using protein domain family resources.

Sayoni Das¹, Christine A Orengo¹

¹Institute of Structural and Molecular Biology, UCL, Gower Street, WC1E 6BT, UK.

Methods (San Diego, Calif.)

|October 6, 2015

Summary

This summary is machine-generated.

Computational methods are crucial for predicting protein functions due to limited experimental data. This review focuses on structure and sequence-based classification for protein function prediction, particularly within the CATH-Gene3D resource.

Keywords:

Moonlighting protein Protein classification Protein family Protein function annotation Protein function prediction

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Last Updated: Apr 1, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

An Integrated Approach for Microprotein Identification and Sequence Analysis

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Published on: July 12, 2022

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Area of Science:

Proteomics
Bioinformatics
Structural Biology

Background:

Vast amounts of protein sequence and structural data are available from genome sequencing and structural genomics projects.
A significant gap exists as only approximately 1% of proteins have experimental functional annotations.
Computational approaches are vital to address the protein annotation gap.

Purpose of the Study:

To review current computational methods for protein function prediction.
To highlight structure and sequence-based classification approaches.
To focus on functional families within the CATH-Gene3D resource.

Main Methods:

Review of existing literature on protein function prediction.
Classification of protein domain families using structural and sequence data.
Analysis of functional families within the CATH-Gene3D database.

Main Results:

Identification of key computational strategies for predicting protein function.
Emphasis on the utility of protein domain family classifications.
Demonstration of the CATH-Gene3D resource's relevance in functional family analysis.

Conclusions:

Computational function prediction is essential given the scale of genomic data.
Structure and sequence-based classification methods offer powerful tools for annotation.
The CATH-Gene3D resource provides a valuable framework for studying protein functional families.