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

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution00:52

¹H NMR of Conformationally Flexible Molecules: Temporal Resolution

1.2K
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
1.2K
Protein Folding01:25

Protein Folding

10.8K
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...
10.8K
Protein Folding01:22

Protein Folding

125.6K
Overview
125.6K
Protein Organization01:24

Protein Organization

8.9K
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....
8.9K
Protein Organization01:13

Protein Organization

155.4K
Overview
155.4K
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR01:15

¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR

1.6K
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
1.6K

You might also read

Related Articles

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

Sort by
Same author

OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling.

Journal of chemical theory and computation·2023
Same author

OPUS-X: an open-source toolkit for protein torsion angles, secondary structure, solvent accessibility, contact map predictions and 3D folding.

Bioinformatics (Oxford, England)·2021
Same author

OPUS-Rota3: Improving Protein Side-Chain Modeling by Deep Neural Networks and Ensemble Methods.

Journal of chemical information and modeling·2020
Same author

OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling.

Journal of chemical theory and computation·2020
Same author

OPUS-Rota2: An Improved Fast and Accurate Side-Chain Modeling Method.

Journal of chemical theory and computation·2019
Same author

Generalized description of spectral incoherent solitons.

Optics letters·2014

Related Experiment Video

Updated: Dec 31, 2025

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

17.5K

OPUS-Refine: A Fast Sampling-Based Framework for Refining Protein Backbone Torsion Angles and Global Conformation.

Gang Xu1, Qinghua Wang2, Jianpeng Ma1,2,3

  • 1Multiscale Research Institute of Complex Systems , Fudan University , Shanghai 200433 , China.

Journal of Chemical Theory and Computation
|January 15, 2020
PubMed
Summary

OPUS-Refine is a novel postprocessing method that enhances protein structure prediction accuracy by refining torsion angles (Phi and Psi) and global configurations. This efficient framework improves predictions from other methods and structural assessments.

More Related Videos

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

69.6K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.9K

Related Experiment Videos

Last Updated: Dec 31, 2025

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

17.5K
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

69.6K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

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

Published on: July 16, 2017

15.9K

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Structure Prediction

Background:

  • Protein backbone torsion angles (Phi and Psi) are fundamental for describing local protein conformation.
  • Accurate prediction of these angles is critical for understanding protein structure and function.

Purpose of the Study:

  • To introduce OPUS-Refine, a general postprocessing method for improving protein structure prediction.
  • To enhance the accuracy of both local (torsion angles) and global protein structural predictions.

Main Methods:

  • OPUS-Refine utilizes a sampling-based approach, incorporating predictions from other methods as constraints.
  • A neighbor-dependent statistical torsion angle sampling database (OPUS-TA) was developed to improve sampling efficiency.
  • Contact maps from RaptorX were integrated as a global structural constraint.

Main Results:

  • Refinement using OPUS-Refine increased the accuracy of Phi/Psi angles predicted by SPIDER3 and SPOT-1D.
  • OPUS-Refine improved global structural accuracy (TM-score, RMSD) and local structural accuracy (Phi/Psi) compared to RaptorX online server predictions.
  • The method demonstrated high efficiency, refining torsion angles in ~4s and global structures in ~30s for a 100-residue protein.

Conclusions:

  • OPUS-Refine is an effective and efficient postprocessing tool for enhancing protein structure prediction accuracy.
  • Its sampling-based nature allows integration with various prediction methods, offering broad applicability.
  • The development of OPUS-TA further supports efficient sampling for related methods.