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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

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

Protein and Protein Structures

Protein and Protein Structures

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.

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Updated: Mar 11, 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

RepeatsDB 2.0: improved annotation, classification, search and visualization of repeat protein structures.

Lisanna Paladin¹, Layla Hirsh^1,2, Damiano Piovesan¹

¹Dept. of Biomedical Sciences, University of Padua, 35121 Padova, Italy.

Nucleic Acids Research

|December 1, 2016

Summary

RepeatsDB 2.0 enhances the database of tandem repeat protein structures with improved annotations for over 5400 proteins. This update offers detailed repeat region information and advanced search capabilities for structural data.

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Last Updated: Mar 11, 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

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

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

Area of Science:

Structural Biology
Bioinformatics
Protein Science

Background:

Repeat proteins are non-globular proteins with diverse functions, implicated in various diseases.
Tandem repeat protein structures are crucial for understanding protein function and disease mechanisms.

Purpose of the Study:

To present RepeatsDB 2.0, an updated and expanded database of annotated tandem repeat protein structures.
To introduce an improved classification schema and enhanced data accessibility for researchers.

Main Methods:

Application of the novel ReUPred annotation method across the Protein Data Bank for extensive repeat unit characterization.
Manual validation of over 60% of entries to ensure high data quality.
Development of a new search engine and redesigned entry pages for improved user experience.

Main Results:

High-quality annotations for approximately 5400 protein structures, including start and end positions for repeat regions and units.
Introduction of a new classification level based on sequence similarity (40%, 60%, 90% identity).
Enhanced comparison features for unit positions, secondary structures, folds, and Pfam domains.

Conclusions:

RepeatsDB 2.0 provides a valuable, comprehensive resource for studying tandem repeat proteins.
The updated database facilitates deeper insights into protein structure-function relationships and disease associations.
Advanced search and visualization tools empower researchers to explore complex structural data efficiently.