TIEO Sonia


************************************************************
		README : dssp_like 
************************************************************





OBJECTIVE
	Secondary structure assignment for proteins in a PDB(Protein Data Bank) file

DESCRIPTION

DSSP (hydrogen bond estimation algorithm) is an algorithm to calculate secondary structure to 	the amino acids of a protein, given the atomic-resolution coordinates of the protein implemented by Wolfgang Kabsch and Chris Sander.

To compare the output of dssp_like, I use mkdssp. ( http://manpages.ubuntu.com/manpages/bionic/man1/dssp.1.html )
Like mkdssp, dssp_like take for entry a protein in the PDB and return an kind of dssp format.



COMMAND LINE (LINUX)
	-------------------------------------------------------------	
	python3 dssp_like.py -i <pdbfile.pdb> -o <outputfile.txt>
	--------------------------------------------------------------

EXAMPLE 
	python3 dssp_like.py -i ~/dssp_like/datas/1bta.pdb -o ~/dssp_like/results/1bta_dssplike.txt


OPTIONS

-i, --input filename

    The file name is a file with typical PDB format and ends with .pdb
    This file needs atom H : if the resolution of the 3D structure doesn't catch H 
    please add the H with reduce (http://kinemage.biochem.duke.edu/software/reduce.php) for example.


-o, --output filename

    The file name of a DSSP file ends with.pdb


-h, --help

    Print the help message and exit. 



DSSP_like FORMATS
.
Column Name  :	Description
RES 	     :  Residue number ( same as PDB file)
AA	     :  The three letter code for the amino acid
STRUCTURE    :
	Sub.Column 1: 
	Code 	Description
	H 	Alpha Helix
	B 	Beta Bridge
	E 	Strand
	G 	Helix-3
	I 	Helix-5
	T 	Turn
	S 	Bend
	Sub.Column 2,3,4: 
	Three column for each of the three n-turns types (n =3, 4 and 5) with '>' if the residue can start a helix and following number  indicates helix type and '<' if residue ends the helix.
BP1 and BP2   :	 The first and second bridge pair candidate


DESCRIPTION OF FOLDERS and FILES INTO dssp_like


* dssp_like/datas
	* pdb files (1bnr.pdb , 1bta.pdb , 2qd4.pdb , 2qd4_withH.pdb) # 2qd4_withH.pdb is transformed by reduce from 2qd4.pdb
	* mkdssp files (1bnr_dssp.txt , 1bta_dssp.txt , 2qd4_withH_dssp.txt )


* dssp_like/results
	* dssp_like file ( 1bnr_dssplike.txt , 1bta_dssplike.txt , 2qd4_withH_dssplike.txt )

* dssp_like.py (Program)

* README

* reduce.3.23.130521 (executable to use if PDB file has no atom H )

* TIEO_rapport_dssp.pdf