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

Cryo-electron Microscopy

Cryo-electron Microscopy

Conventional electron microscopy (EM) involves dehydration, fixation, and staining of biological samples, which distorts the native state of biological molecules and results in several artifacts. Also, the high-energy electron beam damages the sample and makes it difficult to obtain high-resolution images. These issues can be addressed using cryo-EM, which uses frozen samples and gentler electron beams. The technique was developed by Jacques Dubochet, Joachim Frank, and Richard Henderson, for...

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....

Electron Microscope Tomography and Single-particle Reconstruction

Electron Microscope Tomography and Single-particle Reconstruction

Transmission electron microscopy (TEM) can be used to determine the 3D structure of biological samples with the help of techniques such as electron microscope tomography and single-particle reconstruction. While single-particle reconstruction can examine macromolecules and macromolecular complexes in vitro conditions only, tomography permits the study of cell components or small cells in vivo.
Electron Tomography
Electron tomography can be performed either in TEM or STEM (scanning transmission...

You might also read

Related Articles

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

Sort by

Same author

AbTune: layer-wise selective fine-tuning of protein language models for antibodies.

Briefings in bioinformatics·2026

Same author

Molecular insights into the dual-glycoprotein surface layer of the oral bacterium Tannerella serpentiformis.

Journal of molecular graphics & modelling·2026

Same author

Navigating the Pre- and Post-AlphaFold Divide: CAPRI 8th Evaluation Meeting, February 12-14, Grenoble, FR.

Proteins·2025

Same author

Updates to the CASP Infrastructure in 2024.

Proteins·2025

Same author

Improved prediction of antibody and their complexes with clustered generative modelling ensembles.

Bioinformatics advances·2025

Same author

Biomolecular Interaction Prediction in the Pre- and Post-AlphaFold Era: The 8th CAPRI Evaluation.

Proteins·2025

Search research articles

Related Experiment Video

Updated: Dec 29, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

Protein-Protein Modeling Using Cryo-EM Restraints.

Mikael Trellet¹, Gydo van Zundert¹, Alexandre M J J Bonvin²

¹Computational Structural Biology Group, Bijvoet Centre for Biomolecular Research, Faculty of Science-Chemistry, Utrecht University, Utrecht, The Netherlands.

Methods in Molecular Biology (Clifton, N.J.)

|February 2, 2020

Summary

Cryo-electron microscopy (cryo-EM) provides low-resolution maps for molecular modeling. A new protocol uses these maps as restraints in HADDOCK, improving the modeling of complex structures.

Keywords:

Biomolecular interactions Cryo-EM data Flexibility HADDOCK Information-driven docking Molecular modeling

More Related Videos

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

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Related Experiment Videos

Last Updated: Dec 29, 2025

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Author Spotlight: Exploring Cellular Processes by Modeling Ligands in Cryo-EM Maps

Published on: July 19, 2024

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

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Single Particle Cryo-Electron Microscopy: From Sample to Structure

Published on: May 29, 2021

Area of Science:

Structural biology
Biophysics
Computational biology

Background:

Cryo-electron microscopy (cryo-EM) advances enable atomic resolution imaging of molecular complexes.
However, limited resolution in cryo-EM maps, especially in outer regions, hinders detailed atomic structure determination.
Existing modeling approaches often use rigid fitting, neglecting molecular energetics and flexibility.

Purpose of the Study:

To present a novel protocol for modeling molecular complexes using cryo-EM density maps as restraints.
To integrate cryo-EM data into the HADDOCK (High-Ambiguity Driven DOCKing) modeling framework.
To improve the accuracy and completeness of structural models derived from low- to medium-resolution cryo-EM data.

Main Methods:

Utilizing cryo-EM maps as restraints within the HADDOCK 2.4 software.
Employing PowerFit for initial rigid-body fitting to identify molecular positions within the EM map.
Defining distance restraints based on component centers of mass for initial docking.
Incorporating the EM density map as an additional restraint energy term in HADDOCK.

Main Results:

Demonstration of a protocol integrating cryo-EM density maps into HADDOCK for enhanced molecular modeling.
Successful application of EM map restraints to guide the docking process, improving model accuracy.
The protocol leverages both rigid-body fitting and the EM density as a guiding potential.

Conclusions:

The described HADDOCK protocol effectively utilizes low- to medium-resolution cryo-EM maps for molecular modeling.
This approach overcomes limitations of rigid fitting by incorporating energetic and flexibility aspects.
The EM-driven docking protocol offers a valuable tool for structural biologists analyzing cryo-EM data.