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

Genome Annotation and Assembly03:36

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.
Predicting Molecular Geometry02:27

Predicting Molecular Geometry

VSEPR Theory for Determination of Electron Pair Geometries
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.
Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
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 and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

You might also read

Related Articles

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

Sort by
Same author

Advancing impact and access: Introducing <i>JNIS Advances</i>.

Journal of neurointerventional surgery·2026
Same author

Reclassification and weighting of multiple causes of death: US death certificates 2003-2023.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same author

Idiopathic Acquired Hemophilia A With High-Titer Factor VIII Inhibitor in an Elderly Patient: A Case Report.

Cureus·2026
Same author

Silk vista baby versus pipeline embolization device for unruptured distal anterior cerebral artery aneurysms: A multicenter propensity-weighted comparative study.

Journal of neuroradiology = Journal de neuroradiologie·2026
Same author

Toward actionable interventions in human aging (12th ARDD meeting, 2025).

Aging·2026
Same author

Structure-aware graph learning predicts RNA editability across tissues and species.

Research square·2026
Same journal

Chemotactic self-organization captures the dynamics of mammalian hair follicle patterning.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Tomographic imaging of superconducting order using particle-hole interference.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Inferring epidemiological parameters under an infectious phylogeography model with visitor dynamics.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Analytical modeling for suction cup designs for skin-interfaced wearable devices.

Proceedings of the National Academy of Sciences of the United States of America·2026
Same journal

Improving cell-free metabolism through direct integration of artificial respiratory chains.

Proceedings of the National Academy of Sciences of the United States of America·2026
See all related articles

Related Experiment Video

Updated: Jun 26, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Generalized ensemble methods for de novo structure prediction.

Alena Shmygelska1, Michael Levitt

  • 1Department of Structural Biology, Stanford University, Stanford, CA 94305-5126, USA. alena.shmygelska@stanford.edu

Proceedings of the National Academy of Sciences of the United States of America
|January 28, 2009
PubMed
Summary
This summary is machine-generated.

Hamiltonian Replica Exchange Monte Carlo improves protein structure prediction by efficiently searching conformations. This method reveals limitations in the Rosetta energy function, highlighting the importance of specific energy terms for accuracy.

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

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: Jun 26, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
16:41

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

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
  • Structural bioinformatics
  • Protein folding

Background:

  • Protein structure prediction relies on energy functions and conformational search methods.
  • Accurate energy functions and efficient search algorithms are crucial for reliable predictions.
  • Knowledge-based energy functions, like Rosetta, require rigorous testing of their search methodologies.

Purpose of the Study:

  • To evaluate and compare different conformational search methods for protein structure prediction.
  • To rigorously test the Rosetta energy function using advanced search techniques.
  • To identify deficiencies in the Rosetta energy function and improve native-like structure identification.

Main Methods:

  • Implementation of a generalized ensemble search method: Hamiltonian Replica Exchange Monte Carlo.
  • Comparison of Hamiltonian Replica Exchange Monte Carlo with Monte Carlo Simulated Annealing and Temperature Replica Exchange Monte Carlo.
  • Utilizing the Rosetta knowledge-based force field for energy calculations.

Main Results:

  • Hamiltonian Replica Exchange Monte Carlo demonstrates superior performance in sampling low-energy states compared to standard Monte Carlo Simulated Annealing and Temperature Replica Exchange Monte Carlo.
  • The study identified significant deficiencies in the low-resolution Rosetta energy function, as lowest energy structures did not always correspond to native-like structures.
  • Specific energy terms within the Rosetta function, particularly long-range and short-range backbone hydrogen bonding, showed better discrimination between nonnative and native-like structures than the overall low-resolution score.

Conclusions:

  • Advanced generalized ensemble search methods, like Hamiltonian Replica Exchange Monte Carlo, offer improved sampling efficiency for protein structure prediction.
  • The Rosetta energy function exhibits limitations at low resolution, necessitating refinement for accurate prediction of native-like protein structures.
  • Refining the weighting and application of specific energy terms, such as backbone hydrogen bonding, can enhance the accuracy of protein structure prediction using knowledge-based force fields.