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

Overview of Protein Sorting and Transport01:45

Overview of Protein Sorting and Transport

14.5K
Eukaryotic cells have different membrane-bound organelles with distinct protein requirements. The process by which proteins are targeted to a specific organelle is called protein sorting.
Protein sorting can be of two types: signal-based sorting and vesicle-based trafficking. In signal-based sorting, specific amino acid sequences called sorting signals target proteins to the proper location inside the cell either via gated transport or by protein translocation.  In gated transport, folded...
14.5K
Protein Networks02:26

Protein Networks

2.4K
2.4K
Protein Folding01:22

Protein Folding

122.7K
Overview
122.7K
Protein and Protein Structures02:15

Protein and Protein Structures

11.3K
11.3K
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

3.9K
3.9K
Protein Dynamics in Living Cells01:19

Protein Dynamics in Living Cells

2.3K
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...
2.3K

You might also read

Related Articles

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

Sort by
Same journal

A CURE for Microbiology Experiment: Isolation and Characterization of Antimicrobial-Producing Lactic Acid Bacteria From Fermented Sichuan Pickle Against Pathogenic Bacteria.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
Same journal

Innovative Spherical-Shaped Gel Electrophoresis Apparatuses for Scientific Demonstrations to High School Students.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
Same journal

Evaluation of DeepSeek-Generated Biochemistry Clinical Cases for Teaching Purpose.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
Same journal

How Students Use ChatGPT in Biochemistry Education: Evaluating Students' Prompts, Illustrations, and Reflective Assessments as Evidence.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
Same journal

Click Before You Pipette: Building Foundational Pipetting Skills and Confidence With an Interactive Prelaboratory Simulation.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
Same journal

A Semester-Long Laboratory in Molecular Biology and Biochemistry Focusing on the Discovery of Novel β-Lactamase Inhibitors From Streptomyces.

Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology·2026
See all related articles

Related Experiment Video

Updated: Sep 27, 2025

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
05:18

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

Published on: October 20, 2021

2.5K

Visualizing protein big data using Python and Jupyter notebooks.

Charles J Weiss1

  • 1Department of Chemistry and Biochemistry, Augustana University, Sioux Falls, South Dakota, USA.

Biochemistry and Molecular Biology Education : a Bimonthly Publication of the International Union of Biochemistry and Molecular Biology
|April 11, 2022
PubMed
Summary
This summary is machine-generated.

This workshop teaches exploring and visualizing protein data using Python and Jupyter notebooks. Participants discover trends in amino acid abundance and protein structures.

Keywords:
JupyterPDBPythonbig databioinformaticsproteinundergraduate teachingvisualization

More Related Videos

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

209
Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.3K

Related Experiment Videos

Last Updated: Sep 27, 2025

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports
05:18

Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports

Published on: October 20, 2021

2.5K
Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

209
Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches
09:47

Author Spotlight: Advancing Alzheimer's Research – Exploring Early Detection and Multi-Omics Approaches

Published on: December 15, 2023

1.3K

Area of Science:

  • Biochemistry
  • Computational Biology
  • Bioinformatics

Background:

  • The increasing volume of biological data necessitates advanced computational tools for analysis.
  • Protein Data Bank (PDB) data offers rich insights into protein structure and function.
  • Educational initiatives are crucial for equipping scientists with data science skills.

Purpose of the Study:

  • To provide a hands-on workshop experience for exploring and visualizing large protein PDB datasets.
  • To instruct participants on utilizing Jupyter notebooks and Python for biological data analysis.
  • To facilitate the discovery of trends in protein structure and composition.

Main Methods:

  • Utilized Jupyter notebooks and the Python programming language for data analysis.
  • Employed Python functions for loading and manipulating protein PDB data.
  • Applied visualization libraries such as matplotlib and seaborn for data representation.

Main Results:

  • Participants successfully explored large PDB datasets to identify trends.
  • Key trends discovered include amino acid abundance patterns, dihedral angle distributions, and secondary structure frequencies.
  • The workshop successfully demonstrated the utility of Python for biological data exploration.

Conclusions:

  • Jupyter notebooks and Python are effective tools for teaching big data analysis in biochemistry.
  • The freely available resources empower educators and students to explore protein structure data.
  • This approach enhances data literacy and analytical skills in the scientific community.