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

Protein Folding Quality Check in the RER01:29

Protein Folding Quality Check in the RER

ER is the primary site for the maturation and folding of soluble and transmembrane secretory proteins. The calnexin cycle is a specific chaperone system that folds and assesses the confirmation of N-glycosylated proteins before they can exit the ER lumen. The primary players of this quality check pipeline are the lectins, ER-resident chaperones, and a glucosyl transferase enzyme. In case the calnexin system in the lumen fails to salvage a misfolded protein, it is transported to the cytoplasm...
Conservation of Protein Domains Over Different Proteins02:26

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 Organization01:24

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.
Conservation of Protein Domains02:26

Conservation of Protein Domains

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...
Intrinsically Disordered Proteins02:18

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 Proteins02:18

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...

You might also read

Related Articles

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

Sort by
Same author

CASP11 refinement experiments with ROSETTA.

Proteins·2015
Same author

Structure of a designed tetrahedral protein assembly variant engineered to have improved soluble expression.

Protein science : a publication of the Protein Society·2015
Same author

Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy.

Proceedings of the National Academy of Sciences of the United States of America·2015
Same author

Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction.

Chembiochem : a European journal of chemical biology·2015
Same author

Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces.

Science (New York, N.Y.)·2015
Same author

Designing Two-Dimensional Protein Arrays through Fusion of Multimers and Interface Mutations.

Nano letters·2015
Same journal

Thymidylate synthase inhibitory drugs induce p53-dependent pathways differently.

PloS one·2026
Same journal

Top-down and bottom-up attention for joint pattern classification and reconstruction.

PloS one·2026
Same journal

Short- and long-term scaling behavior of blood pressure and pulse arrival time during sleep in healthy controls and patients with obstructive sleep apnea.

PloS one·2026
Same journal

Double DQN-based secrecy energy efficiency and fairness performance in IRS-assisted NOMA systems with friendly jamming.

PloS one·2026
Same journal

10 recommendations for strengthening citizen science for improved societal and ecological outcomes: A co-produced analysis of challenges and opportunities in the 21st century.

PloS one·2026
Same journal

Paying in public: Peer effects, impression management, and willingness to pay on digital payment platforms.

PloS one·2026
See all related articles

Related Experiment Video

Updated: May 30, 2026

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

Modeling disordered regions in proteins using Rosetta.

Ray Yu-Ruei Wang1, Yan Han, Kristina Krassovsky

  • 1Graduate Program in Biomolecular Structure and Design, University of Washington, Seattle, Washington, United States of America.

Plos One
|August 11, 2011
PubMed
Summary
This summary is machine-generated.

Protein structure prediction models can be improved by accounting for configurational entropy, especially in intrinsically disordered proteins. Two Rosetta approaches were tested, with one showing greater practical utility for modeling these flexible regions.

More Related Videos

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

Related Experiment Videos

Last Updated: May 30, 2026

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

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

Area of Science:

  • Computational Biology
  • Biophysics
  • Structural Biology

Background:

  • Protein structure prediction methods like Rosetta typically minimize energy, not free energy.
  • Free energy includes configurational entropy, crucial for understanding protein folding.
  • Disordered protein regions pose challenges as they lack single low-energy conformations.

Purpose of the Study:

  • To develop and evaluate methods within Rosetta for modeling protein regions with significant disorder.
  • To address the limitations of current protein structure prediction that arise from neglecting configurational entropy.

Main Methods:

  • Two Rosetta-based approaches were implemented to handle disordered protein regions.
  • Method 1: Identifies disordered regions by minimizing a free energy function, allowing residues to be ordered or disordered.
  • Method 2: Requires pre-identification of disordered regions (e.g., via DISOPRED or NMR data) and treats them as repulsive during energy calculations.

Main Results:

  • The second approach, requiring prior identification of disordered regions, demonstrated greater practical utility.
  • This method was successfully applied to de novo structure prediction, NMR structure calculation, and comparative modeling.
  • Minimizing free energy, rather than just energy, is essential for accurate protein structure prediction, especially for disordered proteins.

Conclusions:

  • Accurate protein structure prediction requires considering configurational entropy, particularly for intrinsically disordered proteins.
  • Pre-identifying disordered regions and modeling them appropriately within structure prediction software enhances practical utility.
  • The developed Rosetta approaches offer improved modeling capabilities for proteins with flexible or disordered segments.