Introduction to the seminar series
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Introduction to the seminar series. G Vriend. 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. Bioinformatics is everywhere.

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Introduction to the seminar series

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Introduction to the seminar series

G Vriend


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


Bioinformatics is everywhere

Metagenomics related differences


The human genome


Your future in bioinformatics


Part 2Six topics and FF


Six topics

Drug Docking

Homology modelling

Structure validation

Energy calculations and Molecular Dynamics

Force Fields  starting point

Sequence alignment


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.


Part 3A FF we all know


Force Field: weather forecast

So the weather man can predict the wind-direction, but how do we teach a computer to do this?


Force Field: weather forecast


Force Field weather forecast


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 …)


Part 4Definition of a FF


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.


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).


Part 5A FF in chemistry - bioinformatics


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?


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.


Pictures copied from

  • www.almanac.comblogs.parfumswinkel.nl

  • www.ucsd.edubodyfuturist.com

  • www.weerplaza.nlwww.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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