Copyright (C) 2008 Jim Warwicker and Salim Bougouffa

    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.

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    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
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This README relates to the Warwicker laboratory code for simple volume-based
solvation calculations at protein interfaces.

(Manuscript submitted to BMC Bioinformatics: Bougouffa and Warwicker)

Current distribution: June 2008

The shell scripts, Perl code, Fortran code, and this README are in the intcalc.tar
archive.

Assuming that you have unpacked the downloaded archive (e.g. tar xvf intcalc.tar),
then the following will help you.

FIRST, all files, source, compiled programs, data files, output of the
volume solvation 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.
EXCEPT for the input coordinate files, whose path is specified at run time:
perl vol_solvn_loop.pl -i path

SECOND, to build the Fortran programs,

run:		intcalc_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 as:

perl vol_solvn_loop.pl -i (path for pdb files)

Which should return total polar and non-polar solvation volumes for each the
constituents of the complex (12=complex, 1 and 2 are the free components).
These raw numbers can be scaled as described in the manuscript.

The calc_int.list text file specifies what PDB chains make up the 1 and 2 components
of a complex.  In the example file given:
 1b27AD A D
 1CBW A_B_C D

coordinate file 1b27AD.pdb has a complex made from the A (1) and D (2) chains
coordinate file 1CBW.pdb has a complex made from chains A,B,C (1) and chain D (2)


PLANNED UPDATES:

We plan to add post-processing of the raw numbers with the binding model weights
given in the manuscript.

The various sidechain packing algorithms described in the manuscript will be made
available by web-server.

Solvent accessibility features (discussed in the manuscript) will be added.