Bending Residues

DynDom Description

Example Run

  How DynDom Works

DynDom uses the K-means clustering algorithm to find clusters of rotation vectors.

A cluster in rotation space may not correspond to a cluster in real space, but rather a fragmented region. Such a fragmented region one would not normally call a domain. DynDom splits up any clusters that do not correspond to heavy atoms connected through a network of distances of 4.0 angstrom or less, into domains. In order for DynDom to analyse domain pairs in terms of their interdomain movement two criteria must be satisfied. The first concerns the minimum domain size. If a domain comprises fewer residues than the minimum domain size set by the user, then segments from this domain are united with the larger domains they are embedded in. If all the domains from any single cluster are smaller than the minimum domain size, the program stops, unless this is the first cluster found (K=2).

For every domain larger than the minimum size, the program checks which are connected directly through the backbone (not through another domain), and calculates the ratio of interdomain displacement to intradomain displacement for every connected pair. If this ratio is less than the user specified minimum (the second criterion) then this pair are not analysed. The program finds the largest number of clusters for which all connected domain pairs that satisfy both criteria. It is these domain pairs that are analysed in terms of interdomain screw axes, etc. If this is not possible it will analyse any domain pair for interdomain screw axes, etc, provided that the two criteria are satisfied

Bending Residues


(Table of Contents)

Example Run

For further details email : sjh@cmp.uea.ac.uk

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