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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-Protein Interfaces

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Protein-protein Interfaces

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...

Globular and Fibrous Proteins

Globular and Fibrous Proteins

Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...

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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Related Experiment Video

Updated: Jul 4, 2026

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

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

Published on: July 16, 2017

Search strategies in structural bioinformatics.

Mark T Oakley¹, Daniel Barthel, Yuri Bykov

¹School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK.

Current Protein & Peptide Science

|June 10, 2008

Summary

This summary is machine-generated.

This review explores optimization in structural bioinformatics, highlighting Kolmogorov complexity for protein structure comparison and advanced algorithms like the great deluge and memetic algorithms for de novo protein structure prediction.

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

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Published on: April 26, 2013

Area of Science:

Structural Bioinformatics
Computational Biology

Background:

Optimization problems are central to structural bioinformatics.
Recent advancements address key challenges in the field.

Purpose of the Study:

To review recent work on structural bioinformatics challenges.
To highlight novel methods in protein structure comparison and prediction.

Main Methods:

Kolmogorov complexity for protein structure comparison.
De novo protein structure prediction from first principles.
Off-lattice prediction using the great deluge algorithm.
Memetic algorithms for lattice-based protein models.

Main Results:

Kolmogorov complexity proves useful for assessing structural similarity.
The great deluge algorithm aids in off-lattice structure prediction.
Memetic algorithms enhance the study of lattice-based protein models.

Conclusions:

Optimization techniques are crucial for advancing structural bioinformatics.
Novel algorithms offer improved approaches to protein structure comparison and prediction.