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 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...
Protein-protein Interfaces02:04

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...
Protein Folding01:22

Protein Folding

Overview
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...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...

You might also read

Related Articles

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

Sort by
Same author

Elucidating metabolites and biosynthetic pathways during musk maturation: insights from forest musk deer.

Frontiers in pharmacology·2025
Same author

Multiomics analysis provides insights into musk secretion in muskrat and musk deer.

GigaScience·2025
Same author

Efficacy and safety of YOXINTINE for depression: A double-blinded, randomized, placebo-controlled, phase 2 clinical trial.

Phytomedicine : international journal of phytotherapy and phytopharmacology·2024
Same author

Preliminary exploration of the musk biosynthetic mechanism by transcriptomic sequencing in muskrats.

Scientific reports·2024
Same author

Chemical composition and microbiota changes across musk secretion stages of forest musk deer.

Frontiers in microbiology·2024
Same author

Deleterious variant in FAM71D cause male infertility with asthenoteratospermia.

Molecular genetics and genomics : MGG·2024

Related Experiment Video

Updated: Jul 17, 2026

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

Development of a Grid-based statistical potential for protein structure prediction.

Guijun Zhao1, Hui Lu

  • 1Bioinformatics Program, Department of Bioengineering, University of Illinois at Chicago, Chicago, IL 60607 USA.

Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference
|February 7, 2007
PubMed
Summary

This study introduces a new statistical potential for protein structure prediction that considers both residue distance and angle. This method improves the accuracy of identifying native protein structures compared to previous distance-only approaches.

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

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

Related Experiment Videos

Last Updated: Jul 17, 2026

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

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

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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Biophysics

Background:

  • Accurate protein structure prediction is crucial for understanding biological function.
  • Existing statistical potentials primarily rely on residue-pair distances.
  • Incorporating angular information could enhance the accuracy of these potentials.

Purpose of the Study:

  • To explore the angle dependence between residue pairs in protein structures.
  • To develop a novel grid-based statistical potential incorporating both distance and angle information.
  • To evaluate the performance of this new potential against established methods.

Main Methods:

  • Analysis of 1009 non-redundant protein structures.
  • Attachment of local coordinate systems to amino acids to investigate spatial residue distributions.
  • Development of a grid-based statistical potential using a quasi-chemical approximation.
  • Testing the potential on 32 decoy sets.

Main Results:

  • Clear differences in geometric propensities were observed across different spatial grids within the same distance ranges.
  • The developed potential, incorporating distance and angle dependence, correctly identified the native structure as the best scoring in 25 out of 32 decoy sets.
  • Performance was comparable, and in some cases superior, to existing distance-dependent potentials.

Conclusions:

  • Angle dependence is a significant factor in protein residue interactions.
  • The novel grid-based statistical potential offers improved accuracy in protein structure prediction.
  • This approach provides a more refined tool for discriminating native protein conformations.