Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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

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-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...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Faster and More Accurate Estimation of Protein Hinges Based on Information Criteria.

Journal of computational biology : a journal of computational molecular cell biology·2025

Same author

Genetic algorithm-based feature selection with manifold learning for cancer classification using microarray data.

BMC bioinformatics·2023

Same author

More practical differentially private publication of key statistics in GWAS.

Bioinformatics advances·2023

Same author

Privacy-Preserving Statistical Analysis of Genomic Data Using Compressive Mechanism with Haar Wavelet Transform.

Journal of computational biology : a journal of computational molecular cell biology·2022

Same author

Efficient Differentially Private Methods for a Transmission Disequilibrium Test in Genome Wide Association Studies.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing·2021

Same author

Nanopore basecalling from a perspective of instance segmentation.

BMC bioinformatics·2020

Search research articles

Related Experiment Video

Updated: Jun 13, 2026

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

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

Published on: July 16, 2017

Searching protein three-dimensional structures in faster than linear time.

Tetsuo Shibuya¹

¹Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan. tshibuya@hgc.jp

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology

|April 30, 2010

Summary

This study introduces a novel algorithm for efficiently searching 3-D protein structures. The new method significantly improves average-case search times compared to existing algorithms, aiding computational biology research.

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

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

Published on: July 25, 2013

Related Experiment Videos

Last Updated: Jun 13, 2026

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

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

Published on: July 16, 2017

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

Published on: July 8, 2025

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

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

Published on: July 25, 2013

Area of Science:

Computational Biology
Bioinformatics
Structural Biology

Background:

Protein structure comparison is crucial in post-genomic computational biology.
Root Mean Square Deviation (RMSD) is a standard metric for structural similarity.
Finding substructures within a threshold RMSD is a fundamental challenge.

Purpose of the Study:

To develop a faster-than-linear-time average-case algorithm for substructure similarity searching in 3-D protein databases.
To improve upon existing algorithms for large-scale structural comparisons.

Main Methods:

Development of a novel algorithm for substructure searching.
Analysis of the algorithm's average-case time complexity.
Comparison with established worst-case and average-case complexities.

Main Results:

The proposed algorithm achieves an average-case time complexity of O(m + N/m(1-epsilon)).
This represents a significant speed improvement over previous methods.
The algorithm is applicable to other fields like computer vision and robotics.

Conclusions:

The new algorithm offers a substantial advancement in the efficiency of 3-D structure database searching.
It provides a faster solution for identifying similar protein substructures.
This has broad implications for computational biology and related disciplines.