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Related Concept Videos

Protein and Protein Structure02:15

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
Protein and Protein Structures02:15

Protein and Protein Structures

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...

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Updated: Jun 24, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Modeling an Enzyme Active Site using Molecular Visualization Freeware

Published on: December 25, 2021

PDB Editor: a user-friendly Java-based Protein Data Bank file editor with a GUI.

Jonas Lee1, Sung Hou Kim

  • 1Department of Chemistry, University of California, Berkeley, California 94720-5230, USA.

Acta Crystallographica. Section D, Biological Crystallography
|March 25, 2009
PubMed
Summary
This summary is machine-generated.

Protein Data Bank (PDB) file editing is streamlined with PDB Editor, a user-friendly Java application. This software efficiently extracts and manipulates protein structure data, saving researchers valuable time.

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Last Updated: Jun 24, 2026

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Published on: July 12, 2022

Area of Science:

  • Structural Biology
  • Bioinformatics

Background:

  • The Protein Data Bank (PDB) file format is crucial for disseminating and manipulating protein structures.
  • Existing software for editing PDB files is often not user-friendly, leading to significant manual effort for researchers.

Purpose of the Study:

  • To develop a user-friendly software tool for efficient editing and information extraction from PDB files.
  • To provide a stand-alone, platform-independent solution for protein crystallographers and biologists.

Main Methods:

  • Development of PDB Editor using Java Swing GUI.
  • Implementation of parallel search, selection, extraction, and editing functionalities.
  • Creation of a stand-alone application to avoid platform-dependent installation issues.

Main Results:

  • PDB Editor enables users to efficiently search, select, extract, and edit information within PDB files in parallel.
  • The software is a stand-alone Java application, ensuring ease of use across different operating systems.
  • A downloadable version is available at http://sourceforge.net/projects/pdbeditorjl/.

Conclusions:

  • PDB Editor addresses the limitations of existing tools by offering an efficient and user-friendly solution for PDB file manipulation.
  • The software saves researchers significant time and effort in managing protein structure data.
  • PDB Editor promotes wider accessibility and usability in structural biology research.