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molecular structures

Visualize it:  biochemistry games for building skills and making scientific contributions

Todd M. Smith, Sandra G. Porter, Digital World Biology, LLC, Seattle, WA

The wide application of DNA sequencing has made it possible to identify numerous missense mutations.  While it is possible to assign functional consequence to small numbers of changes, understanding why a given change has impact in ways that the can broadly understand is much harder.  This level of translation requires either an in-depth understanding of biochemistry or access to a knowledgebase containing this kind of information. Thus far, neither exist. If we can teach students how to predict the effects of ... Read more



The A, B, Z's of DNA

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.

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Something scary for Halloween - polio virus

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.

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Overcoming Technical Barriers to Incorporate Molecular Structures in Teaching with Molecule World[TM] on the iPad and iPhone

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 ... Read more



Blending art and science to understand genotype and phenotype with public data and Molecule World™ on the iPad

Todd M. Smith, Sandra, G. Porter, Ditigal World Biology LLC. Seattle WA. 

It is impossible to grasp fundamental concepts in biology without understanding the relationship between sequence, structure, and function. Modern data collection technologies are creating enormous data resources that can be used to help students’ understand these relationships, but currently are underutilized. This is due to the fact that easy-to-use tools that meet teachers’ needs for clear instruction and data visualization are not yet commonplace. Filling the gap between the embarrassment of data riches ... Read more



Insulin Folding - see how it's done

This video shows how we used the Molecule World iPad app to make an image of a folded insulin peptide. Protein folding brings the amino acid at the beginning of the protein chain near the amino acid at the other end.

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Exploring the structural basis of the genotype and phenotype relationship with public data and Molecule World[TM] on the iPad

TM. Smith, SG. Porter. Digital World Biology® LLC, Seattle, WA. @finchtalk, @digitalbio  

From plant and animal breeding to genetic modifications to creating new kinds of energy resources, it is impossible to design improvements without understanding the relationship between molecular sequences and their structure and function. As we contemplate new ways to produce food and energy, understanding molecular structures is critical to both target development and follow on manufacturing processes. Additionally, to have large-scale benefit, our emerging scientists, the technical ... Read more



The next generation science standards meet nanopore sequencing

Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS).  According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale."  The authors go on to note that scale and proportion are best understood using the scientific practice of working with models. When scientists and engineers work with these concepts at a molecular scale, new kinds of technologies can be created to advance our understanding of the natural world. One example is DNA ... Read more
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On antiserum and Ebola virus

In 1925, dogsledders raced through the frozen Alaskan bush to bring antiserum to the isolated village of Nome.  The antiserum arrived in time, saved the lives of many villagers from the horrors of diphtheria, and inspired the Iditarod, a famous race in celebration of the dog sledders' heroic feat. West Africa could use a similar effort today.  Richard Harris's blog at NPR has a good story about doctors' efforts to develop and use antiserum to treat Ebola.  According ... Read more
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Increasing the value of genomics and proteomics data with educational applications

Todd M. Smith and Sandra G. Porter, Digital World Biology®, Seattle, WA 

Modern data collection technologies are creating enormous data resources that are underutilized in science education and research. We often present graphs showing exponential growth of one kind of database or another, but how often do we stop to ask the questions: how many people are using these data? And how are they using it? Without efforts toward improving general use, data resources will not be valued, which can negatively impact the value of future data collection endeavors.

New approaches ... Read more



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