A fun thing we can do with molecular models is to create art. In Molecule World™ , the residue coloring option applies a different color to each amino acid and nucleotide. When we're characterizing a protein and trying to understand its function, the residue coloring option helps us identify repetitive or unusual amino acid sequences, but we can also use this coloring option to have fun.
The video at the end shows all the steps put together.
1. Find and download a spherical protein structure.
We created the structure collection feature in Molecule World because I knew it would be useful in teaching my courses. A request from the Weisman Art Museum at the University of Minnesota taught us structure collections could be useful in other ways, too.
The Weisman Art Museum collaborated with neuroscientists at the University of Minnesota and Ricardo Martinez Murillo, a neuroscientist in Spain, to produce the traveling Beautiful Brain exhibit featuring the drawings of Santiago Ramón y Cajal. Cajal is considered the father ... Read more
A few years ago, when the iPhone first came out, I fell in love with an app called "Molecules." It was easy to use, the images were lovely, and I thought manipulating molecules by touch could help solve some of the problems my students had with using Cn3D.
I was all set to switch.
But I couldn't. When it came to teaching, I needed features that Molecules just didn't have.
To make a long story short, we had an SBIR grant from National Science Foundation and the good fortune to work with Molecules' developer and another brilliant engineer to make a new app called " ... Read more
Sandra Porter, Austin Community College and Digital World Biology LLC, Seattle, WA
Our bioinformatics course at Austin Community College focuses on basic concepts and techniques. Students learn how to search databases, use molecular models, apply sequence analysis tools, and characterize genetic variation. Although bioinformatics provides us with interesting real-life examples to study, our abilities are limited when it comes to finding student projects that include opportunities to make new discoveries. We don’t have a lab and we’re not able to generate our own data, so we rely ... Read more
It's well understood in science education that students are more engaged when they work on problems that matter. Right now, Zika virus matters. Zika is a very scary problem that matters a great deal to anyone who might want to start a family and greatly concerns my students. I teach a bioinformatics course where students use computational tools to research biology. Since my students are learning how to use tools that can be applied to this problem, I decided to have them apply their new bioinformatics skills to identify drugs that work against Zika virus. We don't have the lab facilities ... Read more
April 25th (4/25) is national DNA day. Digital World Biology ™ celebrates by sharing some of our favorite DNA structures. We created these photos with Molecule World ™ Molecule World is a tools for exploring molecular and chemical structures on an iPhone or iPad.
When my parents were young, summer made cities a scary place for young families. My mother tells me children were often sent away from their homes to relatives in the country, if possible, and swimming pools were definitely off limits. The disease they feared, poliomyelitis, and the havoc it wrecked were the stuff of nightmares. Children could wake up with a headache and end up a few hours later, in an iron lung, struggling to breathe.
TM. Smith, SG. Porter. Digital World Biology® LLC, Seattle, WA. @finchtalk, @moleculeworld
It is impossible to grasp fundamental concepts of genetic variation without understanding the relationship between sequence, structure, and function. In response to nearly two hundred interviews with KI12 and college teachers and students, we created the Molecule WorldTM iPad and iPhone apps to display 3D-data from multiple structure databases (MMDB, PDB, and PubChem). Molecule World employs a novel rendering engine that allows us to convey depth, and uniquely highlight chemical properties and ... Read more
We feel interesting and sometimes painful sensations when capsaicin, from chilis, and the allyl isothiocyantes from wasabi,bind to receptors in our mouths. In this article, we look at the structures that communicate information to the cell. How do they tell the cell that capsaicin or wasabi compounds are bound? Read more