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

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

Intrinsically Disordered Proteins

Intrinsically Disordered Proteins

Intrinsically disordered proteins are a group of proteins that do not fold into specific three-dimensional structures. Their structural flexibility allows them to complement ordered proteins to perform functions that are inaccessible to rigid structures. They are more common in eukaryotes than prokaryotes and may either be exclusively intrinsically disordered or hybrid proteins, consisting of a mix of ordered and disordered regions. The absence of a rigid structure in these proteins can be...

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...

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.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...

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...

You might also read

Related Articles

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

Sort by

Same author

A Comparative Experimental and Computational Study on the Nature of the Pangolin-CoV and COVID-19 Omicron.

International journal of molecular sciences·2024

Same author

Per Aspera ad Chaos: Vladimir Uversky's Odyssey through the Strange World of Intrinsically Disordered Proteins.

Biomolecules·2023

Same author

A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation.

Biomolecules·2022

Same author

Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2.

Biomolecules·2022

Same author

Characterization of intrinsically disordered regions in proteins informed by human genetic diversity.

PLoS computational biology·2022

Same author

Intrinsically disordered proteins play diverse roles in cell signaling.

Cell communication and signaling : CCS·2022

Search research articles

Related Experiment Video

Updated: May 16, 2026

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

D²P²: database of disordered protein predictions.

Matt E Oates¹, Pedro Romero, Takashi Ishida

¹Department of Computer Science, University of Bristol, Bristol BS8 1UB, UK. Matt.Oates@bristol.ac.uk

Nucleic Acids Research

|December 4, 2012

Summary

The Database of Disordered Protein Prediction (D(2)P(2)) offers a comprehensive resource for analyzing protein disorder across many proteomes. It integrates multiple disorder prediction tools and structural domain data to explore disorder

More Related Videos

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

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

Related Experiment Videos

Last Updated: May 16, 2026

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

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions

Published on: January 26, 2024

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

Area of Science:

Bioinformatics
Computational Biology
Structural Biology

Background:

Intrinsically disordered proteins (IDPs) play crucial roles in cellular functions but are challenging to characterize using traditional structural methods.
Understanding the genomic distribution and evolutionary patterns of protein disorder is essential for comprehending protein function and evolution.

Purpose of the Study:

To present the Database of Disordered Protein Prediction (D(2)P(2)), a centralized resource for analyzing protein disorder across diverse proteomes.
To facilitate large-scale comparisons of various protein disorder prediction methods and their overlap with known protein structures.

Main Methods:

A comprehensive set of protein disorder predictors (VL-XT, VSL2b, PrDOS, PV2, Espritz, IUPred) were applied to all protein sequences from 1765 complete proteomes.
Predicted SCOP (Structural Classification of Proteins) domains from the SUPERFAMILY predictor were integrated with disorder predictions.
Data were made available in downloadable formats (flat files, SQL tables) and through an interactive website with graphical annotations.

Main Results:

The D(2)P(2) database provides integrated disorder and structure annotations for a vast number of proteins.
It enables large-scale comparative analysis of disorder prediction algorithms and their relationship with protein structural domains.
The database facilitates exploration of the genomic distribution and evolutionary context of protein disorder.

Conclusions:

D(2)P(2) serves as a valuable resource for advancing the understanding of the interplay between protein disorder and structure.
The integrated data aids in studying the genomic distribution and evolutionary history of disordered proteins.
The interactive platform supports comparative analysis and exploration of protein disorder across the tree of life.