# Difference between revisions of "Calculating correlated mutations at the protein interface: free energies of pairwise mutants"

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This project will explore the feasibility of calculating residue correlations based on these free energy calculations. From sequence alignmnents and the structure of the complex (for two proteins), we will identify interface contacts and corresponding pairs of mutations that '''do''' occurr in the sequence data, and other pairs of mutations that '''do not''' occur in the sequences. We will then establish if we, as we expect, indeed find a much lower impact on the free energy of the tolerated (''occurring'') pairwise mutations, and a much larger effect than the forbidden (''not occurring'') mutations. | This project will explore the feasibility of calculating residue correlations based on these free energy calculations. From sequence alignmnents and the structure of the complex (for two proteins), we will identify interface contacts and corresponding pairs of mutations that '''do''' occurr in the sequence data, and other pairs of mutations that '''do not''' occur in the sequences. We will then establish if we, as we expect, indeed find a much lower impact on the free energy of the tolerated (''occurring'') pairwise mutations, and a much larger effect than the forbidden (''not occurring'') mutations. | ||

+ | |||

+ | ==Related projects== | ||

+ | * [[Modeling the Effective Interaction Between Proteins - A Coarse-Grained Approach]] |

## Revision as of 14:13, 19 March 2013

Calculating correlated mutations at the protein interface: free energies of pairwise mutants | |
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status: ongoing | |

Master: | project within::Bioinformatics |

Student name: | student name::Helen Kruize |

Dates | |

Start | start date:=2013/04/02 |

End | end date:=2013/06/01 |

Supervision | |

Supervisor: | Anton Feenstra |

Second supervisor: | Qingzhen Hou |

Thesis: | has thesis::Media:Thesis.pdf |

Poster: | has poster::Media:Posternaam.pdf |

#### Signature supervisor

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## Abstract

Correlated mutations have been used for many years to identify functionally crucial residue-pairs, commonly interpreted as well as residue contacts. Recent developments in methods, but mainly the increased size of sequence databases, have made predictions of residue contacts accurate enough to be useful for protein structure and interface predictions.

In (other) recent work, we have showen that using molecular dynamics simulations and a coarse-grained forcefield, we can calculate the free energy barrier for unbinding with accuracy at least similar to that of (much more expensive) atomistic simulations.

This project will explore the feasibility of calculating residue correlations based on these free energy calculations. From sequence alignmnents and the structure of the complex (for two proteins), we will identify interface contacts and corresponding pairs of mutations that **do** occurr in the sequence data, and other pairs of mutations that **do not** occur in the sequences. We will then establish if we, as we expect, indeed find a much lower impact on the free energy of the tolerated (*occurring*) pairwise mutations, and a much larger effect than the forbidden (*not occurring*) mutations.