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Code Listing by David Snyder

Code 1-5 of 5   

The FindCore Toolbox (v. 1.0b)
David Snyder and Gaetano Montelione, (C) 2010

This Matlab Toolbox implements the FindCore algorithm described in Snyder, D.A.; Montelione, G.T. PROTEINS: Struct. Funct. Bioinformaticsm, 2005, 59: 673-86. Clustering algorithms for identifying core atom sets and for assessing the precision of protein structure ensembles. and elsewhere. See the README file for more details.

This toolbox extends the FindCore toolbox by first clustering the input set of structural models (create_multiensemble) and then superimposing each cluster separately. This allows for appropriate assessment of the uncertainty or flexibility in...

The statistics toolbox contains routines for hierarchical clustering, including the cluster routine uses the SAHN tree to group data into clusters. However, the toolbox seems to lack a routine that uses the SAHN tree to describe the hierarchical...

This function performs SAHN clustering (like linkage.m in the Statistics Toolbox) but allows users to define their own inter-cluster distance function. This function is thus more flexible than linkage.m (albeit a lot slower).

(C) 2010...

Input a SAHN tree (e.g. the result of a call to linkage) and the number, n, of clusters into which the SAHN tree is to be partitioned (e.g. by the function cluster). Output is a list of distances where the i'th distance corresponds to cluster i as...