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.
Cytochrome C oxidase is a molecule that none of us air-breathing creatures can live without. It's also really interesting. This protein complex is a dimer of two smaller complexes. Each of the smaller complexes contains 13 different proteins and two heme groups.
Oxidized Cytochrome C Oxidase. Each protein chain is colored differently. Arrows point to the active site in subunit I.
The two heme groups are both part of the cytochrome c oxidase subunit I protein. The DNA sequence of this protein is used for many types of DNA barcoding.
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
BCRs (antibodies) and TCRs (T cell receptors) are the recognition molecules of our immune system; the molecules they bind are called antigens. BCRs and TCRs are similar in many ways, but their differences form the core of how self and non-self are recognized. Read more
Immuno-bioinformatics is a fast growing subdiscipline of immuno-biotechnology. New technologies like immune-profiling and targeted cancer therapies are leading to job growth and demands for new skills and knowledge in biomanufacturing, quality systems, informatics, and cancer biology. Read more
Singularity: the point at which a function takes an infinite value.
"Eew!" Is how high performance computing (HPC) admins react to Docker, according to Dr. Vanessa Saurus when she described the motivation for developing Singularity  at the Cyverse Container Camp . Like Docker, Singularity allows one to package programs and their dependencies in ways that they can be run as virtual instances with low overhead. Singularity improves on Docker to make it possible to run containers in HPC environments such as super computers.
Containerization technologies like Docker are designed to solve challenges associated with installing and running complex software such as bioinformatics pipelines and web servers. Docker will change the world ... maybe. While clearly powerful and enabling, the magic of Docker can also be an overpromise. To understand why, you need to understand the “ The Law of Leaky Abstractions .”
Want to incorporate microbiome and metagenomics research into your lab or teaching? Sign up for the ABRF 2018 microbiome and metagenomics workshop. It may not teach you to zip-line through fire, but you will learn how to generate and manage a fire hose worth of data from microbiome projects. Read more
The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated .” Hmmm. That sounds like bioinformatics.
Surviving the Singularity requires reducing complexity. This was the topic of a recent three-day Cyverse Container Camp hosted at the University of Arizona, Tucson AZ. I attended the camp as part of Digital World Biology's ... Read more