Copyright (C) 2008 Jim Warwicker These programs are free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License. These programs are distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . This README relates to the Warwicker laboratory code for analysing patches in 3D structures, around real and background ('back') phosphorylation sites. Please look at our 2008 BMC Structural Biology article (Kitchen, Saunders and Warwicker) Current distribution: February 2008 The shell scripts, Perl code, Fortran code, and this README are in the phos.tar archive. Assuming that you have unpacked the downloaded archive (e.g. tar xvf phos.tar), then the following will help you. FIRST, all files, source, compiled programs, data files, coordinate files, output of the patches analysis, are currently assumed to be in the working directory. You can play around with the paths in the two Perl programs if you wish. SECOND, to build the Fortran programs, run: patches_build.scr. This uses an F77 compiler; it works on a 32-bit machine running SuSE Linux 9.2, and should be portable at least to other 32 bit Linux systems. THIRD, the analysis is carried out in two stages: run: patches_phos_export.pl input: pdbs.list and pdb files nb CURRENTLY the pdbs.list file, and the psites.list file, use 2 PDB files that are included in this distribution. So you can test the programs before looking at your own data. In the first stage, a list of pdb chains in pdbs.list is analysed through to calculation of patches around ser, thr, tyr residues. These calculations use the compiled Fortran code, (much of which has come from the Warwicker lab electrostatics programs). run: psites_gather_export.pl input: psites.list and output files from the first stage In the second stage, the 'real' phosphorylation sites are separated from the 'back' (background) sites, and a lumped output over the pdb files made. FOURTH, looking at the combined output over PDB files. psites_real.txt and psites_back.txt: Give data for the real and background sites. Each record is the PDB/residue/chain/residue number follwed by 6 columns. The columns record the most positive (mV) potential around that site with 5,10,15,20,25,30 A. So that for the more rightward columns, the search radius is larger and the resulting potentials are larger. psites_real.hist and psites_back.hist Give histograms for the incremental and cumulative data over all real or background sites. Comparison of these will show whether, (at a particular patch radius), real sites are in more +ve environments than background sites.