CDK2 AnalysisΒΆ

Below are the scripts and results for an analysis of Cyclin-Dependent Kinase 2 structure in the PDB carried out in Spring 2012. All files generated can be found in the examples/cdk2 folder of the Polyphony distribution.

  1. Download structures and create an alignment file
polyphony_create_fasta_file.py -p 1HCK -c A -s 95

This command created a file called clust_1HCK_A_95.fasta. (Please note due the limited number of concurrent ftp calls to the RCSD site, this command will need to be run multiple times if you don’t already have the necessary pdb file in the ~/Polyphony/data/pdb folder)

On visualisation with clustalx, it was clear that all sequences in the resulting fasta file were aligned correctly.

For further examples of the use of Polyphony please see the examples directory in the code distribution. This contains the code used to generate the figures in the paper.