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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 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 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 and Protein Structures

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Related Experiment Video

Updated: Jun 8, 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

Pre-calculated protein structure alignments at the RCSB PDB website.

Andreas Prlic¹, Spencer Bliven, Peter W Rose

¹San Diego Supercomputer Center, University of California San Diego, 9500 Gilman Drive, Mailcode 0505 La Jolla, CA 92093-0505, USA. andreas@sdsc.edu

Bioinformatics (Oxford, England)

|October 13, 2010

Summary

A new tool facilitates protein structure comparison by calculating 1D sequence and 3D structure alignments. This aids in discovering relationships within the Protein Data Bank (PDB) and user-submitted proteins.

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Last Updated: Jun 8, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules

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

Published on: July 16, 2017

Area of Science:

Structural Biology
Bioinformatics
Computational Biology

Background:

The Protein Data Bank (PDB) is continuously growing, making comprehensive structure comparisons challenging.
Existing methods may not efficiently handle the scale of the PDB.

Purpose of the Study:

To present a versatile tool for systematic protein structure and sequence comparison.
To support the discovery of novel relationships between protein structures.

Main Methods:

Development of a tool for calculating 1D protein sequence and 3D protein structure alignments.
Implementation of a web service for pairwise alignments.
Provision of a stand-alone application for local analysis and visualization.
Generation of weekly updated, pre-calculated 3D structure comparisons for the entire PDB.

Main Results:

A functional comparison tool is available, supporting various applications.
Users can perform pairwise alignments via a web service or a local application.
Comprehensive, up-to-date 3D structure comparisons of the PDB are accessible.

Conclusions:

The presented tool addresses the challenge of systematic protein structure comparison in a growing PDB.
It enables users to discover new relationships among proteins through sequence and structure alignments.
The tool enhances the utility of the RCSB PDB website and supports independent research.