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Related Concept Videos

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...
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...
Two-Dimensional (2D) NMR: Overview01:12

Two-Dimensional (2D) NMR: Overview

The 1D NMR spectrum of large and complex molecules like natural products has complicated splitting patterns and overlapping signals, which can be easily interpreted using 2-dimensional (2D) NMR. Unlike 1D NMR, 2D NMR has two frequency axes that provide the coupling information between the nucleus A and nucleus B in a molecule. The process from which 2D spectra are obtained has four steps.
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X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
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Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

Different fluorescence-based techniques are used to study the protein dynamics in living cells. These techniques include FRAP, FRET, and PET.
Fluorescent recovery after photobleaching (FRAP) is a fluorescent-protein-based detection technique used to quantify protein movement rates within the cell. This method exposes a small portion of the cell to an intense laser beam. The laser beam causes permanent photobleaching of the fluorophore-tagged proteins in the exposed region. As the bleached...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
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Related Experiment Video

Updated: May 15, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
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Published on: December 25, 2021

ExonVisualiser - application for visualization exon units in 2D and 3D protein structures.

Monika Piwowar1, Porembski Krzysztof, Piwowar Piotr

  • 1Department of Bioinformatics and Telemedicine, Collegium Medicum, Jagiellonian University, Lazarza 16, 31-530 Krakow, Poland.

Bioinformation
|January 1, 2013
PubMed
Summary
This summary is machine-generated.

Exon Visualiser is a web tool that maps exon regions to protein structures. It aids in visualizing gene sequences across primary, secondary, and tertiary protein levels for PDB-deposited proteins.

Keywords:
Exon unit identification in proteinsExon visualisation

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Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • The Exon Visualiser web application facilitates the identification and visualization of protein regions encoded by exons.
  • It supports visualization across primary (sequence), secondary, and tertiary protein structure levels.
  • The tool processes data for genes with protein expressions in the Protein Data Bank (PDB).

Purpose of the Study:

  • To present a novel web application for visualizing the relationship between exons and protein structures.
  • To provide a tool for analyzing protein structures at multiple levels, from sequence to tertiary structure.
  • To enable the correlation of specific exons with corresponding regions in 3D protein structures.

Main Methods:

  • Loading exon sequences and coordinates from GenBank files.
  • Retrieving CDS and amino acid sequences from GenBank and PDB, respectively.
  • Creating a consensus sequence by comparing PDB and GenBank sequences.
  • Matching exon coordinates to protein sequences and visualizing in 2D and 3D.
  • Utilizing color-coded graphical displays to link protein structures with exons.

Main Results:

  • Successful implementation of a web application for exon-protein structure visualization.
  • The Exon Visualiser enables detailed analysis of protein structures based on exon data.
  • Color-coded graphical displays highlight the correlation between exons and protein chains in 3D structures.

Conclusions:

  • The Exon Visualiser is a valuable tool for researchers studying gene-protein structure relationships.
  • It enhances the understanding of how exon organization influences protein architecture.
  • The application provides a user-friendly interface for exploring complex genomic and proteomic data.