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 Organization01:13

Protein Organization

Overview
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 Organization01:13

Protein Organization

Overview
Protein Folding01:25

Protein Folding

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...
Protein Folding01:22

Protein Folding

Overview

You might also read

Related Articles

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

Sort by
Same author

Tracking DOT1L methyltransferase activity by stable isotope labelling using a selective synthetic co-factor.

Communications chemistry·2024
Same author

Publisher Correction: Decoding chromatin states by proteomic profiling of nucleosome readers.

Nature·2024
Same author

Decoding chromatin states by proteomic profiling of nucleosome readers.

Nature·2024
Same author

A framework to predict the price of energy for the end-users with applications to monetary and energy policies.

Nature communications·2021
Same author

Threshold Static Automated Perimetry of the Full Visual Field in Idiopathic Intracranial Hypertension.

Investigative ophthalmology & visual science·2019
Same author

An Integrated Chemical Proteomics Approach for Quantitative Profiling of Intracellular ADP-Ribosylation.

Scientific reports·2019

Related Experiment Video

Updated: Jun 20, 2026

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

Selecting high quality protein structures from diverse conformational ensembles.

Ashwin Subramani1, Peter A DiMaggio, Christodoulos A Floudas

  • 1Department of Chemical Engineering, Princeton University, Princeton, New Jersey, USA.

Biophysical Journal
|September 16, 2009
PubMed
Summary

A novel clustering method, ICON, effectively identifies protein structures closest to the native state from large ensembles. This computational approach significantly improves accuracy in protein structure prediction challenges.

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

Related Experiment Videos

Last Updated: Jun 20, 2026

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

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

Area of Science:

  • Computational Biology
  • Structural Bioinformatics
  • Protein Science

Background:

  • Protein structure prediction is crucial for understanding biological function.
  • Identifying the native protein structure from an ensemble of predicted models is a key challenge.
  • Existing methods often struggle with accuracy across varying decoy resolutions.

Purpose of the Study:

  • To address the challenge of identifying native-like protein structures from large ensembles.
  • To introduce a novel iterative clustering method based on the Traveling Salesman Problem.
  • To evaluate the performance of the proposed method across diverse datasets.

Main Methods:

  • Developed an iterative clustering algorithm (ICON) utilizing Traveling Salesman Problem principles.
  • Employed statistical analysis of cluster density and average spherical radius for iterative refinement.
  • Tested ICON on four diverse datasets including high and medium-to-low resolution decoys.

Main Results:

  • ICON successfully identified high-quality, native-like structures across all tested datasets.
  • The method demonstrated robustness irrespective of the resolution of the predicted conformers.
  • Selected conformers by ICON were consistently within the top 3.5% of the ensemble on average.

Conclusions:

  • ICON provides an effective solution for selecting native-like structures in protein structure prediction.
  • The iterative clustering approach enhances the accuracy of identifying correct protein folds.
  • ICON's performance across varied decoy resolutions highlights its broad applicability.