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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 Organization

Protein Organization

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,...

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Related Experiment Video

Updated: Jul 9, 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

SIMAP--structuring the network of protein similarities.

Thomas Rattei¹, Patrick Tischler, Roland Arnold

¹Chair of Genome Oriented Bioinformatics, Center of Life and Food Science, Technische Universität München, 85350 Freising-Weihenstephan, Germany.

Nucleic Acids Research

|November 27, 2007

Summary

The Similarity Matrix of Proteins (SIMAP) database offers pre-calculated protein sequence similarities and features for millions of proteins. This resource aids evolutionary and functional analysis, accessible via a web portal and web services.

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Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Protein sequence analysis is crucial for understanding protein evolution and function.
Computational analysis of large protein datasets is resource-intensive.
Existing databases may lack comprehensive, pre-calculated similarity data.

Purpose of the Study:

To establish the Similarity Matrix of Proteins (SIMAP) database.
To provide a comprehensive, up-to-date resource of pre-calculated protein sequence similarity matrices.
To offer sequence-based features, such as InterPro domains, for all major public protein sequences.

Main Methods:

Compilation of protein sequences from major public databases.
Calculation of a comprehensive sequence similarity matrix.
Annotation of protein sequences with InterPro domains (version 16).
Development of a portlet-based web portal for data visualization and access.
Integration of protein clusters and a novel search for similar domain architectures.

Main Results:

SIMAP covers approximately 17 million proteins and over 6 million non-redundant sequences as of September 2007.
Provides pre-calculated similarity data and InterPro domain annotations.
Features a user-friendly web portal with structured views.
Offers programmatic access through Web Services.

Conclusions:

SIMAP serves as a valuable, freely accessible resource for academic research in protein science.
Facilitates computationally intensive sequence analysis tasks.
Enhances the study of protein evolution, function, and domain architectures.