Coarse grained protein simulation

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About Coarse grained protein simulation


Description

Background

Coarse-grained models of proteins and protein aggregation

In their natural cellular environment proteins are dissolved in a concentrated aqueous solution of biomolecules. Even under such crowded conditions, proteins must not aggregate; aggregates may be cytotoxic or compromise the biological function of the proteins. Evolutionary pressure generally ensures that proteins do not aggregate in their natural biochemical environment. A well-known mechanism to prevent aggregation is the folding of proteins.

What needs to be done

The aim of the research is to investigate under which conditions, and with which sequences, proteins are prone to aggregate. Your job is to either investigate this with an exisiting protein model, or, if you are a strong programmer, to further develop the simulation model.


Requirements

  • an interest to work with toy models of protein structures
  • ability to read (and write) C++ code