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

Conserved Binding Sites01:49

Conserved Binding Sites

4.3K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.3K
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
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
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Leaky Scanning02:28

Leaky Scanning

5.2K
During most eukaryotic translation processes, the small 40S ribosome subunit scans an mRNA from its 5' end until it encounters the first start AUG codon. The large 60S ribosomal subunit then joins the smaller one to initiate protein synthesis. The location of the translation initiation is largely determined by the nucleotides near the start codon as there may be multiple translation initiation sites present on the mRNA.  Marilyn Kozak discovered that the sequence RCCAUGG (where R...
5.2K
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

You might also read

Related Articles

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

Sort by
Same author

A multimodal AI biomarker PATH-ORACLE improves prediction of recurrence in stage I lung adenocarcinoma.

medRxiv : the preprint server for health sciences·2026
Same author

Histopathology and proteomics are synergistic for high-grade serous ovarian cancer platinum response prediction.

NPJ precision oncology·2025
Same author

ViralPrimer: a web server to monitor viral nucleic acid amplification tests' primer efficiency during pandemics, with emphasis on SARS-CoV-2 and Mpox.

Bioinformatics (Oxford, England)·2024
Same author

Exploring the Effectiveness of Acyclovir against Ranaviral Thymidine Kinases: Molecular Docking and Experimental Validation in a Fish Cell Line.

Life (Basel, Switzerland)·2024
Same author

Frequent CHD1 deletions in prostate cancers of African American men is associated with rapid disease progression.

NPJ precision oncology·2024
Same author

Transfer learning may explain pigeons' ability to detect cancer in histopathology.

Bioinspiration & biomimetics·2024

Related Experiment Video

Updated: Aug 6, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.3K

SARS-CoV-2 receptor-binding domain deep mutational AlphaFold2 structures.

Oz Kilim1, Anikó Mentes1, Balázs Pál1,2

  • 1Department of Physics of Complex Systems, Eötvös Loránd University, Budapest, Hungary.

Scientific Data
|March 15, 2023
PubMed
Summary
This summary is machine-generated.

This study used AlphaFold2 to create a comprehensive dataset of SARS-CoV-2 spike protein mutations, aiding future variant prediction and understanding protein structure-genotype-phenotype relationships.

More Related Videos

Engineering Antiviral Agents via Surface Plasmon Resonance
13:00

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

2.4K
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.5K

Related Experiment Videos

Last Updated: Aug 6, 2025

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

4.3K
Engineering Antiviral Agents via Surface Plasmon Resonance
13:00

Engineering Antiviral Agents via Surface Plasmon Resonance

Published on: June 14, 2022

2.4K
Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy
14:55

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Published on: September 17, 2017

15.5K

Area of Science:

  • Virology
  • Structural Biology
  • Computational Biology

Background:

  • The SARS-CoV-2 virus rapidly evolves, necessitating tools for predicting new variants.
  • Understanding the structural impact of mutations is crucial for tracking viral evolution.

Purpose of the Study:

  • To generate a comprehensive structural dataset of all single mutations in the SARS-CoV-2 spike protein receptor-binding domain (RBD) across major lineages.
  • To assess the reliability of AlphaFold2 predictions for mutant structures and their correlation with protein dynamics.
  • To provide a resource for accelerating virology research and variant prediction.

Main Methods:

  • Utilized AlphaFold2 (AF2) for computational modeling of SARS-CoV-2 spike protein RBD mutations.
  • Generated 26,733 Protein Data Bank (PDB) structures representing single mutations from 7 main SARS-CoV-2 lineages.
  • Analyzed AlphaFold2's per-residue confidence scores (pLDDT) and compared them with protein disorder approximations.

Main Results:

  • Created a complete, curated dataset of 26,733 SARS-CoV-2 RBD mutant PDB structures.
  • Demonstrated a correlation between AF2 pLDDT values and protein disorder approximations, suggesting capture of internal protein dynamics.
  • Established the utility of structural and phenotype data combined with machine learning for virology research.

Conclusions:

  • The generated structural dataset provides insights into the SARS-CoV-2 mutational landscape.
  • AlphaFold2 can model protein dynamics, aiding in the understanding of genotype-phenotype relationships.
  • This resource accelerates research into viral evolution and future variant prediction.