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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




Part 2 six topics and ff

Part 2Six topics and FF


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.


Part 3 a ff we all know

Part 3A FF we all know


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 …)


Part 4 definition of a ff

Part 4Definition of a FF


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).


Part 5 a ff in chemistry bioinformatics

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 molecule?

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 molecule?

  • 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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