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-protein Interfaces02:04

Protein-protein Interfaces

14.3K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
14.3K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

4.2K
4.2K

You might also read

Related Articles

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

Sort by
Same author

DeepRank-Ab: a scoring function for antibody-antigen complexes based on geometric deep learning.

Communications biology·2026
Same author

Accurate Physics-Based Flexible Docking of Macrocyclic Ligands.

Journal of medicinal chemistry·2026
Same author

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

Proteins·2025
Same author

Towards better structural models from cryo-electron microscopy data with physics-based methods.

FEBS letters·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

Related Experiment Video

Updated: Dec 3, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

10.9K

PDB-tools web: A user-friendly interface for the manipulation of PDB files.

Brian Jiménez-García1, João M C Teixeira2, Mikael Trellet1

  • 1Bijvoet Centre for Biomolecular Research, Utrecht University, Utrecht, The Netherlands.

Proteins
|October 28, 2020
PubMed
Summary

This study introduces PDB-Tools Web, an online service for manipulating Protein Data Bank (PDB) files. This tool simplifies complex structural data editing through a user-friendly interface and over 40 integrated tools.

Keywords:
PDBbioinformaticsstructural biologyweb server

More Related Videos

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.9K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K

Related Experiment Videos

Last Updated: Dec 3, 2025

Modeling an Enzyme Active Site using Molecular Visualization Freeware
14:37

Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

10.9K
Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
09:51

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

15.9K
Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
05:00

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs

Published on: August 9, 2024

1.7K

Area of Science:

  • Structural Biology
  • Bioinformatics
  • Computational Chemistry

Background:

  • The Protein Data Bank (PDB) format is crucial for representing macromolecular structures but is prone to manual editing errors.
  • Existing software toolkits aid PDB file manipulation but lack a centralized, accessible online platform.
  • There is a need for a user-friendly online solution to streamline PDB file processing.

Purpose of the Study:

  • To develop and present PDB-Tools Web, a flexible and accessible online service for manipulating PDB files.
  • To provide a graphical user interface that simplifies the combination of multiple PDB manipulation tools.
  • To enable users to perform complex PDB data processing, visualization, and download through a single web platform.

Main Methods:

  • Development of a web server integrating the pdb-tools suite.
  • Implementation of a rich, user-friendly graphical interface for tool selection and pipeline creation.
  • Integration of online visualization and download capabilities for processed PDB files.

Main Results:

  • PDB-Tools Web offers a flexible online service for PDB file manipulation.
  • Users can combine over 40 individual tools from the pdb-tools suite via a graphical interface.
  • Complex processing pipelines can be created, saved, uploaded, and their results visualized and downloaded online.

Conclusions:

  • PDB-Tools Web provides a valuable, accessible online resource for researchers working with macromolecular structures.
  • The platform simplifies complex PDB file editing and analysis, overcoming the limitations of manual methods.
  • This tool enhances the efficiency and ease of PDB data manipulation for the scientific community.