Code and datafiles with PNAS publication "Defining a new nomenclature for the structures of active and inactive kinases"

We are providing Perl scripts and data files required to perform clustering reported in PNAS manuscript "Defining a new nomenclature for the structures of active and inactive kinases". Following is a brief description of the uploaded files:

1. kinasefamilylist.txt - List of protein kinases analyzed in the study with their Uniprot, gene names and domain boundaries.

2. kinasepmlz.pl: Perl script which uses PSI-BLAST to identify and download the protein kinase structures from PDB. It also updates the residue numbering scheme of downloaded PDBs with Uniprot numbering scheme.

3. readsiftz.pl: Perl script to download Sifts files for all the PDBs in study to get the residue correspondence between PDB numbering and Uniprot numbering scheme for all the kinases.

4. dfg.pl: Perl script that reads data file containing kinase structure list and dihedral angles of residues (kinasedata.txt) and prints distance matrix. This distance matrix is used as an input to dbscan function in fpc package in R.

5. kinasedata.txt: Data file containing list of kinases with dihedral angles of residues used in clustering. This data file is the input for the script dfg.pl.