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BioInteractive

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Chemspace

More About Chembank

In the future, as the various interactions and properties of small molecules are discovered, they will be entered into a comprehensive database known as Chembank. One nascent idea of the use of Chembank data is that molecules can be plotted at certain points in “chemical space.” The three-dimensional plot shown here is an example of a chemical space plot. Chemical space has many possible dimensions—as many as there are properties in the database. Because of the high dimensionality, each axis shown here corresponds to a combinations of certain subsets of molecular properties such as size, dipole moment, etc.

Hypothetically, molecules that affect a specific aspect of biology may appear in different regions of chemical space. Sometimes they may be dispersed, or sometimes they may be clustered. In this example series of chemical space plots, hypothetical molecules affecting diabetes (including rapamycin and SMIR) are plotted in green, and those that affect cell division (including furrowstatin) are plotted in pink. The regions of the chemical space occupied by these molecules can be thought of as “biology space,” or more specifically, “diabetes space,” and “cell division space.” Such a graphic concept could be a useful tool for understanding biological functions, or finding molecules that affect specific biological functions.

Chemical Space Background

Genbank is the annotated NIH genetic sequence database of all publicly available DNA sequences. There is an initiative in chemical genetics to build an analogous “Chembank.” Chembank is envisioned to be a freely-available collection of data about small molecules, with an emphasis on their effects on biology. The project is in an early stage, but eventually it is planned to be a comprehensive resource for structures, properties, and biological effect of chemical compounds.

Chemical Space Teaching Tips

The animations in this section have a wide variety of classroom applications. Use the tips below to get started but look for more specific teaching tips in the near future. Please tell us how you are using the animations in your classroom by sending e-mail to biointeractive@hhmi.org.

  1. Use the animations to make abstract scientific ideas visible and concrete.

  2. Explain important scientific principles through the animations. For example, the biological clocks animations can be used to demonstrate the fundamentals of transcription and translation.

  3. Make sure that students learn the material by repeating sections of the animations as often as you think necessary to reinforce underlying scientific principles. You can start, restart, and play back sections of the animations.

  4. Urge students to use the animations in accordance with their own learning styles. Students who are more visually oriented can watch the animations first and read the text later, while others might prefer to read the explanations first and then view the graphics.

  5. Incorporate the animations into Web-based learning modules that you create to supplement your classroom curricula.

  6. Encourage students to incorporate the animations into their own Web-based projects.

Resources

HHMI's 2002 Holiday Lectures on Science "Scanning Life's Matrix: Genes, Proteins and Small Molecules"

Chemical Space Credits

Director: Dennis Liu, Ph.D.

Scientific Direction: Stuart L. Schreiber, Ph.D.

Scientific Content: Satoshi Amagai, Ph.D.

Animator: Eric Keller

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Additional Materials

Bulletin Article