Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

Protein Organization

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 Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein Organization

Protein and Protein Structure

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...

Protein and Protein Structures

Protein and Protein Structures

You might also read

Related Articles

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

Sort by

Same author

Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets.

bioRxiv : the preprint server for biology·2026

Same author

Systematic discovery of pro- and anti-HIV host factors in primary human CD4+ T cells.

Cell·2026

Same author

A Dose-Finding Design for Drug Combinations Using a Bayesian 4 Parameter Logistic Model With Penalised D-Optimality.

Pharmaceutical statistics·2026

Same author

The scientific legacy of Martin Karplus from the perspective of his collaborators.

Biophysical journal·2026

Same author

Phase 1 study of ceralasertib, an ATR kinase inhibitor, in combination with durvalumab in patients with recurrent or metastatic NSCLC or HNSCC.

British journal of cancer·2026

Same author

The filamentous ultrastructure of the PopZ condensate is required for its cellular function.

Nature structural & molecular biology·2026

Same journal

De Novo Protein Design Using the Blueprint Builder in Rosetta.

Current protocols in protein science·2020

Same journal

Methods for Expression of Recombinant Proteins Using a Pichia pastoris Cell-Free System.

Current protocols in protein science·2020

Same journal

Histone Purification Combined with High-Resolution Mass Spectrometry to Examine Histone Post-Translational Modifications and Histone Variants in Caenorhabditis elegans.

Current protocols in protein science·2020

Same journal

A Rapid and Facile Purification Method for Glycan-Binding Proteins and Glycoproteins.

Current protocols in protein science·2020

Same journal

Synthesis of Recombinant Human Hemoglobin With NH<sub>2</sub> -Terminal Acetylation in Escherichia coli.

Current protocols in protein science·2020

Same journal

A Fluorescence-Based Assay to Monitor SUMOylation in Real-Time.

Current protocols in protein science·2020

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Comparative Protein Structure Modeling Using MODELLER.

Benjamin Webb¹, Andrej Sali¹

¹University of California at San Francisco, San Francisco, California.

Current Protocols in Protein Science

|November 2, 2016

Summary

This summary is machine-generated.

This study explains comparative protein structure modeling, a method to predict protein 3D structures using known structures. It details using MODELLER software and the ModBase database for accurate modeling.

Keywords:

MODELLER ModBase comparative modeling protein fold protein structure structure prediction

More Related Videos

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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

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

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

Published on: July 16, 2017

Related Experiment Videos

Last Updated: Mar 12, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction

A Protocol for Computer-Based Protein Structure and Function Prediction

Published on: November 3, 2011

Application of I TASSER, trRosetta, UCSF Chimera, HADDOCK server, and HEX loria for De Novo and In Silico Design of Proteins

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

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

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

Published on: July 16, 2017

Area of Science:

Structural bioinformatics
Computational biology
Protein modeling

Background:

Comparative protein structure modeling leverages known protein structures (templates) to predict the 3D structure of a target protein sequence.
The process involves key steps: fold assignment, target-template alignment, model building, and model evaluation.

Purpose of the Study:

To describe the calculation of comparative protein models using MODELLER software.
To explain the utilization of the ModBase database for accessing these models.
To discuss the four core steps of comparative modeling, common errors, and practical applications.

Main Methods:

Utilizing the MODELLER software package for comparative protein structure modeling.
Employing the ModBase database for retrieving and analyzing protein models.
Detailed explanation of fold assignment, target-template alignment, model building, and model evaluation.

Main Results:

Successful application of MODELLER for comparative modeling, exemplified by lactate dehydrogenase from Trichomonas vaginalis (TvLDH).
Guidance provided on downloading and installing the MODELLER software.
Comprehensive discussion of the comparative modeling workflow and potential pitfalls.

Conclusions:

Comparative modeling with MODELLER and ModBase provides a robust approach for predicting protein structures.
Understanding the steps and potential errors is crucial for generating reliable protein models.
The described methods and tools have broad applications in structural biology and drug discovery.