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

6.6K
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....
6.6K
Newman Projections02:06

Newman Projections

17.0K
Different notations are used to represent the three-dimensional structure of molecules on two-dimensional surfaces. One of the most commonly used representations is the dash-wedge formula. The dashed wedges, solid wedges, and the plane lines indicate the groups situated behind the plane, coming out of the plane, and in the plane, respectively.
The organic molecules rotate across the single bonds leading to numerous temporary three-dimensional structures of varying energy known as...
17.0K
Globular and Fibrous Proteins02:21

Globular and Fibrous Proteins

43.9K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
43.9K
Protein Folding01:22

Protein Folding

118.6K
Overview
118.6K
Fischer Projections02:18

Fischer Projections

13.5K
Learning to draw Fischer projections of molecules and understanding their relevance plays a crucial role in the visual depiction of organic molecules. A Fischer projection is a two-dimensional projection on a planar surface to simplify the three-dimensional wedge–dash representation of molecules. This is especially helpful in the case of molecules with multiple chiral centers that can be difficult to draw. Here, all the bonds of interest are represented as horizontal or vertical lines.
13.5K
Gene Families01:57

Gene Families

8.9K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
8.9K

You might also read

Related Articles

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

Sort by
Same author

Three-dimensionally printed mesoporous bioactive glass for craniomaxillofacial bone regeneration: Material evolution, functional mechanisms, and clinical translation.

Cell transplantation·2026
Same author

CryoFSL: an annotation-efficient, few-shot learning framework for robust protein particle picking in cryo-electron microscopy micrographs.

Briefings in bioinformatics·2026
Same author

Proton-coupled alternating access in a versatile mycobacterial Spns drug transporter.

bioRxiv : the preprint server for biology·2026
Same author

Oxidative stress-induced endothelial dysfunction drives mechanical and infectious lung injury: Therapeutic potential of kaempferol in males.

Redox biology·2026
Same author

On the state of protein function prediction: a report on the fourth CAFA challenge.

bioRxiv : the preprint server for biology·2026
Same author

Integrating protein and DNA embeddings for improving genome-wide transcription factor binding site prediction.

NAR genomics and bioinformatics·2026

Related Experiment Video

Updated: Jul 31, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.0K

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer.

Tianqi Wu1, Zhiye Guo1, Jianlin Cheng1

  • 1Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211, United States.

Bioinformatics (Oxford, England)
|May 5, 2023
PubMed
Summary
This summary is machine-generated.

ATOMRefine is a new deep learning method that refines protein structures predicted by tools like AlphaFold. This method improves atomic accuracy and fixes errors, enhancing the usability of predicted protein models for research.

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

68.8K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

437

Related Experiment Videos

Last Updated: Jul 31, 2025

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures
10:10

Neutron Crystallography Data Collection and Processing for Modelling Hydrogen Atoms in Protein Structures

Published on: December 1, 2020

5.0K
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

68.8K
Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function
05:57

Author Spotlight: In Silico Creation and Impact of Carbonylated Amino Acids on Protein Structure and Function

Published on: April 26, 2024

437

Area of Science:

  • Computational Biology
  • Structural Biology
  • Biophysics

Background:

  • State-of-the-art protein structure prediction methods like AlphaFold are crucial for biomedical research.
  • Improving the quality and accuracy of predicted protein structures is essential for their practical application.
  • Current methods require enhancement to ensure the nativeness and usability of predicted protein models.

Purpose of the Study:

  • To develop ATOMRefine, a deep learning-based method for refining all-atom protein structural models.
  • To enhance the accuracy and quality of protein structures predicted by existing tools.
  • To provide a fast and effective solution for correcting structural errors in predicted protein models.

Main Methods:

  • Developed ATOMRefine, an end-to-end, all-atom protein structural model refinement method.
  • Utilized a SE(3)-equivariant graph transformer network to directly refine atomic coordinates.
  • Trained and tested on AlphaFoldDB, CASP14 regular targets, and CASP14 refinement targets.

Main Results:

  • ATOMRefine significantly improves the quality of both backbone and all-atom conformations of AlphaFold-predicted structures.
  • Outperformed two state-of-the-art refinement methods across multiple evaluation metrics, including the MolProbity score.
  • Demonstrated effectiveness in refining protein geometry and fixing structural errors through direct coordinate refinement.

Conclusions:

  • ATOMRefine offers a viable and rapid solution for enhancing the accuracy of predicted protein structures.
  • The method improves the usability of predicted protein models by refining atomic details and correcting errors.
  • ATOMRefine provides a valuable tool for structural biologists and researchers working with predicted protein structures.