*****************************************
>SequenceRetrieving
method		input						change this parameter with -r option of JET. See usage of JET to obtain description of this parameter
format		fasta						fasta: fasta input file, fasta: fasta input file
*****************************************
>QBlast					
eValue 		1.0E-5						psiblast maximum expected value threshold
results		20000	            				maximum number of results 
url 		http://www.ncbi.nlm.nih.gov/BLAST/Blast.cgi	BlastQ server URL
database 	nr						database used
matrix 		blosum62					matrix used to fetch homologs
gap_existence	11						BLOSUM62=11, PAM30=9, BLOSUM45=15, PAM70=BLOSUM80=10  
gap_extension	1						BLOSUM62=1, PAM30=1, BLOSUM45=2, PAM70=BLOSUM80=1
max_iter	3						number of iteration for psi-blast
****************************************
>PDB
url		http://www.rcsb.org/pdb/downloadFile.do		URL of PDB server

*****************************************
>Filter
min_identity	0.20						min sequence identity
max_identity	0.98						max sequence identity
*****************************************
>Sample
length_cutoff	0.8						minimum sequence length expressed in number of residues	
						
*****************************************
>Software
clustalW	/usr/local/bin/clustalw2			clustalW system dependent command
muscle		/usr/bin/muscle			 		muscle system dependent command
naccess		/opt/JET2/naccess2.1.1/naccess			naccess system dependent command
psiblast	/opt/blast-2.2.27+/bin/psiblast 		psiblast system dependent command     
*****************************************
>Data
substMatrix	/opt/JET2/matrix				directory location of matrices used in JET (Blosum62, gonnet and hsdm)
blastDatabases	/disk1/blastdb/					directory location of databases used for local blast (nr{0-7})

*****************************************
>ET
coverage	0.99999						maximum coverage percentage of trace
freq_cutoff	0.0						minimum frequency of trace residue
msaNumber	-1						number of alignments (trees), -1 for JET computting
seqNumber	-1						number of sequences in alignments, -1 for JET computting

*****************************************
>Access
probe_radius	1.4						radius of probe used for accessible surface detection
res_cutoff	0.05						minimum percentage accessible surface of a residu
atom_cutoff	0.01						minimum accessible surface of an atom 
accessType	chain						change this parameter with -d option of JET. See usage of JET to obtain description of this parameter

*****************************************
>CV
max_dist        20.0                                            max distance 
*****************************************
>Interface
cutoff		0         					minimum percentage accessible surface variation of an interface residu
ligand		no						(yes|no) keep contact of ligand (SUBSTRATE, PRODUCT and COFACTOR of database ENZYME) to compute interface of protein
enzymeCpd	/opt/JET/jet/data/enzyme.txt			location of file containing database ENZYME
homologousPDB	no						(yes|no) add interface residues of homologous structures (find in pdb database clustered at 95% of identities) to interface of protein
clusteredPDB	/opt/JET/jet/data/clusters95.txt		location of pdb database clustered at 95% of identities

*****************************************
>Cluster
max_dist	5.0						max distance between atoms to aggregate
analysis	2						change this parameter with -a option of JET. See usage of JET to obtain description of this parameter
namePcCol	pc						name of the column in results file containing the phisical-chemical score of residues (do not change this parameter)
namePcLCol       pcL                                            name of the column in results file containing the residues propensities to be found at prot-lig interfaces (do not change this parameter)
nameTraceCol	trace						name of the column in results file containing the conservation score of residues (do not change this parameter)
coverage	-1						change this parameter with -s option of JET. See usage of JET to obtain description of this parameter
	
