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

Conservation of Protein Domains Over Different Proteins

Conservation of Protein Domains Over Different Proteins

Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...

Conservation of Protein Domains

Conservation of Protein Domains

Protein Complex Assembly

Protein Complex Assembly

Protein Complex Assembly

Protein Complex Assembly

Proteins can form homomeric complexes with another unit of the same protein or heteromeric complexes with different types. Most protein complexes self-assemble spontaneously via ordered pathways, while some proteins need assembly factors that guide their proper assembly. Despite the crowded intracellular environment, proteins usually interact with their correct partners and form functional complexes.
Many viruses self-assemble into a fully functional unit using the infected host cell to...

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

You might also read

Related Articles

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

Sort by

Same author

Search, organize, aggregate and share image data with BioFile Finder (BFF).

Nature methods·2026

Same author

A conserved antioxidant defense at the endoplasmic reticulum membrane.

Cell reports·2026

Same author

Phenotypic landscape of an invasive fungal pathogen reveals its unique biology.

Cell·2025

Same author

Colony context and size-dependent compensation mechanisms give rise to variations in nuclear growth trajectories.

Cell systems·2025

Same author

Comparing simulations of actin filament compression reveals tradeoff between computational cost and capturing supertwist.

microPublication biology·2025

Same author

Phenotypic landscape of a fungal meningitis pathogen reveals its unique biology.

bioRxiv : the preprint server for biology·2024

Search research articles

Related Experiment Video

Updated: Apr 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

Multidomain Assembler (MDA) Generates Models of Large Multidomain Proteins.

Samuel Hertig¹, Thomas D Goddard¹, Graham T Johnson²

¹Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California; Resource for Biocomputing, Visualization, and Informatics, University of California, San Francisco, San Francisco, California.

Biophysical Journal

|May 9, 2015

Summary

We created MULTIDOMAIN ASSEMBLER (MDA) to improve protein structure prediction for large, multi-domain proteins. MDA automates template selection and model generation, addressing challenges in complex protein modeling.

More Related Videos

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Related Experiment Videos

Last Updated: Apr 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

Analyzing and Building Nucleic Acid Structures with 3DNA

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Interactome-Seq: A Protocol for Domainome Library Construction, Validation and Selection by Phage Display and Next Generation Sequencing

Published on: October 3, 2018

Area of Science:

Computational biology
Structural bioinformatics
Protein modeling

Background:

Homology modeling is crucial for predicting protein structures.
Modeling proteins with multiple domains presents unique challenges, including spatial arrangement and template selection.
Existing methods struggle with proteins containing numerous domains or a vast number of potential templates.

Purpose of the Study:

To develop an automated tool for homology modeling of multi-domain proteins.
To address challenges in template searching, selection, and spatial arrangement for complex protein structures.
To integrate this tool into the UCSF CHIMERA molecular graphics package.

Main Methods:

Developed MULTIDOMAIN ASSEMBLER (MDA) software.
Automated template searching, visualization, and selection processes.
Implemented multidomain model generation within UCSF CHIMERA.

Main Results:

MDA effectively handles proteins with a large number of domains (e.g., fibronectin).
The software addresses template coverage issues for regions with varying homology.
Successful demonstration of applications and discussion of MDA's capabilities.

Conclusions:

MULTIDOMAIN ASSEMBLER (MDA) is a valuable tool for homology modeling of complex, multi-domain proteins.
MDA automates and improves critical steps in the protein structure prediction pipeline.
The software offers solutions for challenges related to template selection and spatial arrangement in large proteins.