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Presentation Transcript

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

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.

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

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 …)

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).

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?

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.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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