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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 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 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...

Protein and Protein Structures

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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.
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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.
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Updated: Jun 6, 2025

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

DescribePROT Database of Residue-Level Protein Structure and Function Annotations.

Bi Zhao¹, Sushmita Basu², Lukasz Kurgan³

¹Genomics program, College of Public Health, University of South Florida, Tampa, FL, USA.

Methods in Molecular Biology (Clifton, N.J.)

|November 22, 2024

Summary

DescribePROT is a new online database offering 13 protein descriptors at the amino acid level for 1.4 million proteins. This resource aids in understanding protein function and developing new structure prediction tools.

Keywords:

Amino acids Database Intrinsic disorder Machine learning Prediction Protein Protein function Protein structure Secondary structure Solvent accessibility ligand binding

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Last Updated: Jun 6, 2025

A Protocol for Computer-Based Protein Structure and Function Prediction

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Published on: November 3, 2011

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Published on: July 16, 2017

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

Published on: July 25, 2013

Area of Science:

Biochemistry and structural biology
Bioinformatics and computational biology
Proteomics

Background:

Proteins are fundamental biological molecules with complex structures and functions.
Understanding protein characteristics at the amino acid level is crucial for biological research and drug development.
Existing resources may lack comprehensive, integrated data on diverse protein descriptors.

Purpose of the Study:

To introduce DescribePROT, a freely available online database.
To provide access to a wide range of structural and functional protein descriptors.
To facilitate research in protein function elucidation, therapeutic development, and predictor evaluation.

Main Methods:

Developed a database integrating 13 diverse protein descriptors.
Included sequence conservation, secondary structure, solvent accessibility, and interaction sites.
Processed 1.4 million proteins from 83 complete proteomes.
Implemented a graphical interface for data visualization and interaction.

Main Results:

DescribePROT offers 7.8 billion predictions for 1.4 million proteins.
The database covers 83 complete proteomes of model organisms.
Data is downloadable at multiple scopes and accessible via an interactive graphical interface.

Conclusions:

DescribePROT serves as a valuable resource for researchers studying protein structure and function.
The integrated descriptors can advance the development of novel protein predictors.
Future expansion plans aim to further enhance the database's utility.