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

You might also read

Related Articles

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

Sort by
Same author

Foldify: Web Application for Protein Structure Prediction.

Journal of chemical information and modeling·2026
Same author

C-terminal long-QT type 1 R562S-Kv7.1 variant, the first variant in helix C impairing β-adrenergic response of the slow delayed rectifier K+ channel.

Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology·2026
Same author

MolMeDB RDF: transforming a relational database about biological membranes to the RDF format to increase interoperability.

Journal of cheminformatics·2026
Same author

PROPTIMUS LIVE: local constrained α-carbon optimization of proteins.

Nucleic acids research·2026
Same author

Dense yet flexible: how ladderanes found in anammox bacteria impact phospholipid membrane structure and properties.

Physical chemistry chemical physics : PCCP·2026
Same author

Atomic Charge Calculator III: a modern platform for calculating partial atomic charges.

Nucleic acids research·2026
Same journal

Correction to 'scSuperAnnotator: A platform for benchmarking comparison and visualizing automated cellular annotation methods for scRNA-seq data'.

Nucleic acids research·2026
Same journal

Correction to 'Differentiable partition function calculation for RNA'.

Nucleic acids research·2026
Same journal

Deployment of non-canonical splicing in tunicate genomes is mediated by divergent U2AF function and changing m6A modification in U1 and U6 snRNA.

Nucleic acids research·2026
Same journal

Bacillus subtilis DnaB forms multiple protein-protein interactions essential for DNA replication initiation.

Nucleic acids research·2026
Same journal

Multiple forms of protein-protein and DNA binding are exhibited by BrxC from the BREX phage restriction system.

Nucleic acids research·2026
Same journal

Biosynthesis of glycosylated 5-hydroxycytosine in the DNA of diverse viruses.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 6, 2026

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
07:55

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

Published on: March 7, 2019

8.4K

PDBsum additions.

Tjaart A P de Beer1, Karel Berka, Janet M Thornton

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK and Department of Physical Chemistry, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacký University Olomouc, tř. 17. listopadu 12, 771 46 Olomouc, Czech Republic.

Nucleic Acids Research
|October 25, 2013
PubMed
Summary
This summary is machine-generated.

PDBsum website offers enhanced protein structure analysis tools. New features include human protein variant annotation and dynamic domain relationship graphs for better protein data exploration.

More Related Videos

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.3K

Related Experiment Videos

Last Updated: May 6, 2026

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe
07:55

A Deep-sequencing-assisted, Spontaneous Suppressor Screen in the Fission Yeast Schizosaccharomyces pombe

Published on: March 7, 2019

8.4K
Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance
04:58

Author Spotlight: Investigating the Role of Repetitive DNA Misregulation in Cancer Initiation and Immunotherapy Resistance

Published on: December 13, 2024

3.8K
Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.3K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Biology

Background:

  • The Protein Data Bank (PDB) is a crucial repository for macromolecular structures.
  • Effective visualization and analysis tools are essential for interpreting PDB data.
  • PDBsum provides pictorial analyses of PDB entries, aiding structural understanding.

Purpose of the Study:

  • To introduce and describe the latest features and enhancements to the PDBsum website.
  • To improve the accessibility and depth of analysis for protein structure data.
  • To offer new tools for exploring protein sequences, domains, ligands, and structural features.

Main Methods:

  • Integration of human protein sequence annotations, including naturally occurring amino acid variants.
  • Development of dynamic graphs to visualize relationships between protein domain architectures.
  • Implementation of analyses for ligand binding clusters across multiple experimental structures.
  • Inclusion of analyses for tunnels within protein structures.
  • Introduction of new search functionalities for PDBsum.

Main Results:

  • PDBsum now offers comprehensive annotation of human protein sequences with genetic variations.
  • Dynamic graphs facilitate the understanding of protein domain evolution and relationships.
  • Ligand binding site comparisons are now possible across different structural studies of the same protein.
  • Analysis of protein tunnels provides insights into molecular pathways and dynamics.
  • Enhanced search capabilities improve data retrieval and user experience.

Conclusions:

  • The updated PDBsum website provides advanced tools for structural biologists and bioinformaticians.
  • New features enhance the exploration of protein structure, function, and variation.
  • PDBsum continues to be a valuable resource for the structural biology community.