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

7.2K
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....
7.2K
Protein Organization01:13

Protein Organization

123.3K
Overview
123.3K
Protein Organization01:13

Protein Organization

19.5K
19.5K
Protein Organization01:24

Protein Organization

9.0K
9.0K
Protein and Protein Structures02:15

Protein and Protein Structures

14.6K
14.6K
Protein and Protein Structure02:15

Protein and Protein Structure

71.5K
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...
71.5K

You might also read

Related Articles

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

Sort by
Same author

Engineering Symbiotic Nitrogen Fixation for Agriculture: Predominant Role of Host Plants and Fine-Tuning Regulation.

Plants (Basel, Switzerland)·2026
Same author

Dango: Predicting higher-order genetic interactions.

Cell systems·2026
Same author

Structural insights into insect-selective sodium channel toxins drive AI-enhanced biopesticide design.

Nature communications·2026
Same author

Unified modeling of 3D molecular generation via atomic interactions with PocketXMol.

Cell·2026
Same author

Immunogenicity and Safety of Two-dose Schedules With Different Intervals of an ORF7-deficient Live Vaccine Candidate for Varicella: A Randomized, Double-blind, Controlled, Phase 2b Trial.

The Pediatric infectious disease journal·2026
Same author

<i>iMeta</i> Conference 2025: Creating high-impact international journals.

iMeta·2025

Related Experiment Video

Updated: May 2, 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

70.1K

RaptorX server: a resource for template-based protein structure modeling.

Morten Källberg1, Gohar Margaryan, Sheng Wang

  • 1Toyota Technological Institute, Chicago, IL, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 28, 2014
PubMed
Summary

The RaptorX server offers automated protein structure prediction, aiding biologists in understanding protein function. This computational tool models protein structure, even for distantly related sequences, accelerating biological discovery.

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

1.3K
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

16.2K

Related Experiment Videos

Last Updated: May 2, 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

70.1K
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

1.3K
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

16.2K

Area of Science:

  • Structural biology
  • Computational biology
  • Bioinformatics

Background:

  • Determining the function of newly discovered proteins is essential in modern biology.
  • Computational modeling of protein 3D atomic structure is crucial for understanding protein roles.
  • Existing methods face challenges in predicting structures for proteins with distantly related known structures.

Purpose of the Study:

  • To present the RaptorX server, a web-based protocol for automated protein structure prediction.
  • To enable accurate secondary and tertiary structure modeling using template-based approaches.
  • To facilitate the assignment of functional properties to novel proteins.

Main Methods:

  • Developed a community-wide web-based protocol named RaptorX server.
  • Implemented automated protein secondary structure prediction.
  • Utilized template-based tertiary structure modeling and probabilistic alignment sampling.
  • Employed a novel nonlinear context-specific alignment potential and probabilistic consistency algorithm for detecting remote template sequences.

Main Results:

  • The RaptorX server accurately predicts secondary and tertiary protein structures.
  • It successfully detects remotely related template sequences, even with distant evolutionary relationships.
  • High-quality structural models can be generated for proteins with limited experimentally solved homologous structures.
  • Prediction of a 200 amino acid protein sequence takes approximately 30 minutes.

Conclusions:

  • The RaptorX server provides a valuable tool for automated protein structure prediction.
  • It enhances the ability to determine protein function by providing accurate structural models.
  • This protocol supports biological research by making protein structure prediction more accessible and efficient.