Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

20.4K
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...
20.4K
Intrinsically Disordered Proteins02:18

Intrinsically Disordered Proteins

2.9K
2.9K
Protein Organization01:24

Protein Organization

9.9K
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....
9.9K
Protein Folding01:25

Protein Folding

12.0K
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
12.0K
Protein Folding01:22

Protein Folding

129.4K
Overview
129.4K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.9K
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...
14.9K

You might also read

Related Articles

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

Sort by
Same author

Neck region-microtubule interactions direct counterclockwise stepping of kinesin-1.

Biophysical journal·2026
Same author

Mechanistic principles of antimicrobial peptides uncovered by charge density-based machine learning.

Chemical communications (Cambridge, England)·2026
Same author

Modern machine learning methods for protein property prediction.

Current opinion in structural biology·2025
Same author

Allosteric changes in the conformational landscape of Src kinase upon substrate binding.

Journal of molecular biology·2024
Same author

Generative artificial intelligence for small molecule drug design.

Current opinion in biotechnology·2024
Same author

Author Correction: PLAS-20k: Extended Dataset of Protein-Ligand Affinities from MD Simulations for Machine Learning Applications.

Scientific data·2024

Related Experiment Video

Updated: Mar 7, 2026

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.9K

Computer Simulations of Intrinsically Disordered Proteins.

Song-Ho Chong1, Prathit Chatterjee1, Sihyun Ham1

  • 1Department of Chemistry, Sookmyung Women's University, Yongsan-Ku, Seoul 04310, Korea;

Annual Review of Physical Chemistry
|February 23, 2017
PubMed
Summary

Investigating intrinsically disordered proteins (IDPs) requires new methods. This review covers advances in force fields and computational techniques to link protein disorder to function.

Keywords:
configurational entropycorrelation entropyforce fieldmolecular dynamicsstatistical thermodynamics

More Related Videos

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

17.7K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

1.2K

Related Experiment Videos

Last Updated: Mar 7, 2026

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments
09:25

Author Spotlight: Exploring Intrinsically Disordered Protein Dynamics Through NMR Relaxation Experiments

Published on: November 1, 2024

2.9K
Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
10:58

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

Published on: July 25, 2013

17.7K
Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins
05:08

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

1.2K

Area of Science:

  • Structural biology
  • Molecular dynamics
  • Protein folding

Background:

  • Intrinsically disordered proteins (IDPs) lack stable structures, complicating their study.
  • Connecting the structural disorder of IDPs to their biological function is a key challenge.
  • Traditional methods struggle with the dynamic and heterogeneous nature of IDPs.

Purpose of the Study:

  • To review recent advancements in computational methods for studying IDPs.
  • To highlight the development and evaluation of molecular mechanics force fields for IDPs.
  • To explore methods for calculating protein configurational entropy and its link to IDP function.

Main Methods:

  • Molecular dynamics (MD) simulations for atomic-level characterization.
  • Statistical thermodynamics for thermodynamic descriptions.
  • Development and critical evaluation of molecular mechanics force fields.
  • Computational approaches for protein configurational entropy estimation.

Main Results:

  • IDPs are sensitive to inaccuracies in molecular mechanics force fields, posing simulation challenges.
  • Advances in force fields are crucial for accurate structural characterization of IDPs.
  • New computational methods offer thermodynamic insights into protein configurational entropy.
  • These methods aim to bridge the gap between structural disorder and protein activity.

Conclusions:

  • Accurate force fields and advanced computational methods are essential for understanding IDPs.
  • Molecular dynamics and statistical thermodynamics provide powerful tools to complement experimental studies.
  • Progress in calculating protein configurational entropy offers a thermodynamic link to IDP function.