cosurim Files

Program:	cosurim, v1o17 
A program for the computation of residues and  classes specific compositions 
of CORE and SURFACE from x-ray structures. Both absolute and normalized compositions are computed.
It redirects two outputs:
one for single PDB (useful for individual analysis)
other for all PDBs (useful for statistical analysis)

User parameters:
---modes: "cs" (CORE-SURF) and "csr" (CORE-RIM-SURF)
--upper limit of core (ulc), upper limit for RIM (ulr): adjustable by USERs (see below);
--between CORE and SURF, a rim region can be set by using appropriate option,
 to separate CORE and SUFR regions and to determine its compositions.

Authors:	Parth Sarthi Sen Gupta, Rifat Nawaz Ul Islam and Amal Kumar Bandyopadhyay
Interpretor:	AWK - Aho AV, Kernighan BW, Weinberger PJ 1977
Citation:	Tsodikov et al [2002],Journal of computational chemistry. 23,600-609
IMPORTANT:  
The program "SURFACE RACER" by the above author, is used to compute analytical
relative-residue-accessibility. So USERs of this automation are requested to
cite the above reference.

bugs and suggestions:	akbanerjee[at]biotech[dot]buruniv[dot]ac[dot]in;



OPERATION PRINCIPLE
The automation first makes list of all PDBs, present in the working directory of the program. 
Each PDB file is then splits into chains,
For each chain of the PDB, 
using the USER INPUT, it determines the mode of calculation,
-if "cs", the program  divided the protein structure into CORE and SURFACE regions
the SIZE of the core is determined by the user parameter: "ulc"
-if "csr", the program  divided the protein structure into CORE, RIM and SURFACE
the SIZE of the core and rim are determined by user parameters: "ulc" and "ulr"
---then residue's-relative RSA is computed.
---using the user provided parameters, "ulc" (for "cs") or  "ulc" and "ulr" (for "csr")
the program determines the absolute and normalized compositions for
----------------residues
----------------and their classes (hydrophobic, acidic, basic, polar etc)
if the PDB file name is xxxx.pdb, the output here is xxxx.xls,
where these results are stored.
The program also redirect another output named "total.xls"
It contains PDB's chain-specific compositional analysis
[it would be helpful to find mean observations, for all PDBs,
that are belonging to an ORTHOLOGOUS CLADE]
It helps compositional analysis on proteomic scale.

the program continues this way, until all PDBs are completed.


Installation:
download the program and README file (this one).
keep them in a directory/folder.
unzip 
In CYGWIN (32 bit), open C-SHELL and 
type: "./cosurim and then  enter
[the program runs using the provided PDB file: xxxx.pdb;
and redirect two outputs, xxxx.xls and total.xls]

end of readme