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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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goals
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
Bioinformatics is everywhere

Metagenomics related differences

six topics
Six topics

Drug Docking

Homology modelling

Structure validation

Energy calculations and Molecular Dynamics

Force Fields  starting point

Sequence alignment

qc force field
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
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 forecast3
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
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 general1
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).

slide18

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?

slide19

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
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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