• Skip to main content
  • Skip to primary sidebar
  • Skip to footer

eagereyes

Visualization and Visual Communication

  • Explore
    • Starter Pack
    • Blog Calendar
    • Blogroll
    • eagereyesTV YouTube Videos
  • Practical
    • Basics
    • Pie Charts
    • Techniques
    • Book Reviews
    • Journalism
  • Academic
    • Speaking Mistakes
    • Acceptance Rates
    • Papers
    • Conference Reports
    • Lists of Influences
    • Criticism
    • Peer Review
  • Admin
    • About
    • Contact
    • License

Robert Kosara / March 24, 2010

A Visual Language for Proteins: Jane Richardson

Proteins

Proteins are among the most complex structures we know. They consist of thousands of atoms, and fold into complex shapes to perform a variety of functions. Understanding how they work is not possible from looking at single atoms, but rather at the overall, three-dimensional structure. The visual language for doing this was developed by Jane Richardson.

I find it fascinating to learn that concepts and ideas that I take for granted were only invented relatively recently. When we look at visualizations of proteins today, we expect clean, relatively simple shapes: ribbons, helices, and the rope-like structures that connect them. But this is a very abstracted view that was not at all obvious thirty years ago.

Scientists only figured out how to determine the three-dimensional structure of proteins in the 1970s. When Jane Richardson was writing a review article about the proteins whose structure was known in 1980, she needed a consistent way of showing them. It was clearly not very practical (or useful for understanding) to draw thousands of atoms that were part of a complex, three-dimensional structure.

Protein as atoms and abstracted

There are three distinct structures in a protein: alpha-helices (spiral shapes), beta sheets (ribbons), and turns (the “ropes” in-between). Seeing those in the atom structure (above) is almost impossible, but crucial for understanding how a protein works.

Jane Richardson’s contribution was finding a visual way of representing these components of proteins. Her ribbon diagrams simplify the structure of the protein, and at the same time focus on the important parts. These diagrams were hand-drawn at first; today, any program that shows proteins includes this style of showing them, they are used in textbooks, etc.

I interviewed Richardson for the Sightings column in American Scientist a while ago. She is a professor at Duke University and still uses visual means (virtual reality, among them) for teaching and research to further our understanding of complex molecules.


This is my entry for Ada Lovelace Day 2010.

Teaser image: left part by Jane S. Richardson, right part by Wikipedia user Debstar. Atoms-to-abstraction image by Wikipedia user Opabinia regalis

Filed Under: Blog 2010

Robert Kosara is Senior Research Scientist at Tableau Software, and formerly Associate Professor of Computer Science. His research focus is the communication of data using visualization. In addition to blogging, Robert also runs and tweets. Read More…

Reader Interactions

Comments

  1. Hadley Wickham says

    March 24, 2010 at 5:27 pm

    Does anyone else find the hand drawn version to be far more aesthetically appealing? I don’t like the heavily saturation and high gloss of the computer generated examples.

    Reply
  2. Robert Kosara says

    March 25, 2010 at 10:25 am

    I completely agree. I actually spent some time googling for better computer-generated images, but couldn’t find any. I also implemented a ribbon visualization a while ago for a company, and used less saturated colors there. But they were still a bit on the glossy side and didn’t have the charm of the hand-drawn ones. It would take using some more advanced CG techniques to make these things look better, but it’s definitely doable. Glossy, high-contrast, primary colors are definitely easier to do, though.

    Reply
  3. Nathan says

    March 25, 2010 at 1:54 pm

    the hand-drawn ones look way better. that’s often the case, i think. i mean, if a person can draw well in the first place, i’d always put my money on him/her vs a programmer.

    Reply

Leave a Reply Cancel reply

This site uses Akismet to reduce spam. Learn how your comment data is processed.

Primary Sidebar

More Blog 2010 Articles

  • HTML5 and Visualization on the Web
  • My Journey to the Kingdom of NIPS
  • Stories Don’t Tell Themselves
  • Blogging BOF at VisWeek
  • The Theory Guide to VisWeek 2010

Recently Popular

  • Data: Continuous vs. Categorical
  • The Simple Way to Scrape an HTML Table: Google Docs
  • Understanding Pie Charts
  • Spreadsheet Thinking vs. Database Thinking
  • How The Rainbow Color Map Misleads
  • What is Visualization? A Definition
  • Stacked Bars Are the Worst
  • Facebook
  • GitHub
  • LinkedIn
  • RSS
  • Twitter
  • YouTube

Subscribe via Email

Footer

  • About
  • Contact
  • License

Copyright © 2006–2021 Robert Kosara · All original materials are available under CC-BY-SA