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Introduction to the seminar series

Explore how chemists, mathematicians, & physicists contribute to bioinformatics through topics like Drug Docking, Molecular Dynamics, & more. Learn about the concept of Force Fields and their application in predicting system behaviors. Discover how approximations and sub-forces are utilized in energy calculations. Discover insights on predicting the wind direction in weather forecasts. Dive into the fundamentals of Force Fields and their role in describing and predicting system behaviors. Delve into Force Fields in chemistry and bioinformatics, and how they calculate the energy minimum of molecules using sub-forces like electrostatic attraction. Join us in this enlightening seminar series to enhance your understanding of bioinformatics and Force Fields' significance.

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Introduction to the seminar series

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  1. Introduction to the seminar series G Vriend

  2. Goals • Illustrate a series of bioinformatics areas in which chemists, mathematicians, and physicists can constructively contribute (and find jobs…) • Explain the very generally applicable concept: Force Field

  3. Bioinformatics is everywhere Metagenomics related differences

  4. The human genome

  5. Your future in bioinformatics

  6. Part 2Six topics and FF

  7. Six topics Drug Docking Homology modelling Structure validation Energy calculations and Molecular Dynamics Force Fields  starting point Sequence alignment

  8. QC -> Force Field Quantum chemistry is accurate, but slow. But… everything larger than a hydrogen must be calculated using approximations. And often these approximations take the form of a Force Field.

  9. Part 3A FF we all know

  10. Force Field: weather forecast So the weather man can predict the wind-direction, but how do we teach a computer to do this?

  11. Force Field: weather forecast

  12. Force Field weather forecast

  13. Force Field weather forecast The weather forecast Force Fields thus needs: A description of the weather now (… present situation …) Examples of how the weather evolved in the past from many different starting situations (… to learn from …) A computer program (… that holds the rules …)

  14. Part 4Definition of a FF

  15. Force Field general More general a Force Field consists of data and a set of associated rules that can be used to describe a system and predict its future.

  16. Force Field general More general a Force Field consists of data and a set of associated rules that can be used to describe a system and predict its future. So you can use a Force Field to say if a system is normal or exceptional (for a molecule that would be in or near the energy minimum versus in an excited state) and how a system will develop (for a molecule that would be calculating the energy minimum given an excited state).

  17. Part 5A FF in chemistry - bioinformatics

  18. Force Field to calculate the energy minimum of a protein molecule? Hint, we cannot use QC, so we must make approximations. One idea would be to decompose the total force on each atom in sub-forces like electrostatic attraction/repulsion, etc. Which sub-forces can you think of?

  19. Bond-length sub-force If we assume the bond (length) and the forces over the bond to behave like a spring And please remember that the energy is the integral over the force. This will come back in the Molecular Dynamics seminar.

  20. Pictures copied from • www.almanac.com blogs.parfumswinkel.nl • www.ucsd.edu bodyfuturist.com • www.weerplaza.nl www.cancer.gov • www.cawcr.gov.au • www.crystalinks.com • www.mgms.org • Brucetarrpaintings.org • kniga-ryby-rossii.prv.pl • Nothinginbiology.org

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