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 <http://www.gnu.org/licenses/>.

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.