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A Rotamer Library optimized for Protein Docking

The interaction of proteins is biologically important, e.g. for the regulation of metabolical proteins. The prediction wether and how two proteins interact is neccessary for drug design. During interaction, proteins have to be flexible to fulfill their task in metabolism. These phonomenon is kwon as induced fit. One kind of flexibility is the local movement of side chains. The aim of the project is to investigate flexibility of proteins during docking.

Difference of
  Chi1 angle docked/undockedDistribution of Chi1 angle of Arginine

A Rotamer library describes the conformation of amino-acid side chains and the associated probabilities. Amino acids have up to four possible torsions within their side chain, depending on the residue. These torsions are described by the Chi angles. Former Rotamer libraries where established for folding prediction, the statistics do not include Residues of a nearby second protein which influences the conformation of the Residues of the investigated protein. The new Rotamer library models the influence of nearby residues on the conformation of the actual residue. The probabilities for a discrete set of chi angles is investigated with the help of Bayes Statistics.

The new rotamer library will model the dependencies of the Chi angles on the secondary structure (described by the backbone angles), the previous Chi angle and the angles of amino acids close to the actual residue.

This project is supported by the DFG graduate program Structure Formation.

sneumann@TechFak.Uni-Bielefeld.DE Last Update: 18 Dec 02