SPIN-beta-1.1
Written by Suk Hoon Jung {sh.jung@kaist.ac.kr}
Last modified: 2009-01-13
Last modified: 2009-06-11
1. conf/spin.properties: configuration file that should be changed before running.
spin.db.host = localhost
// MySQL host
spin.db.port = 3306
// MySQL port
spin.db.name = spin
// MySQL db name
spin.db.user = root
// MySQL db user
spin.db.password = xxxxxxx
// MySQL db password
#Mutually Exclusive Domain-Domain Interactions Bin (MEDDIbin)
spin.meddi.backup = Y
// make backup table or not
#Mutually Exclusive Protein-Protein Interactions Bin (MEPPIbin)
spin.meppi.input = mipsInteraction.sif
// input file
spin.meppi.usepredifinedmeddi = Y
// use predefined ME DDIs or not
spin.meppi.ddi.backup = Y
// make backup table or not for ME DDIs
spin.meppi.ppi.backup = Y
// make backup table or not for ME PPIs
#SPIN generation (SPINbin)
spin.spinbin.folder = spin
2.
// folder in which generated SPINs saved
Mutually Exclusive PPI pair generation
A.
Modify conf/spin.properties
B.
Run MEDDIbin.java
i.
Input
1.
Table Psimap : a table includes information on interfacial residues from
analyzing PDB entities.
ii.
C.
Output
1.
Progress while running
2.
Summary of the result
3.
Table, ddi_mei
Run MEPPIbin.java
i.
Input
1.
Interaction file
2.
Table mips2swp: id mapping table (MIPS->SwissProt)
3.
ii.
3.
Table swp2scop: protein domain assignment table (Swissprot: scop families)
Output
1.
Summary of the result
2.
Table ppi_mei
SPIN generation
A.
Modify conf/spin.properties
B.
Run MEDDIbin.java
C.
Run SPINbin.java
i.
Input
1.
2.
Parameters
A.
None: run test PPIN from file named spin_smaple.sif
B.
One parameter: specify input PPIN file.
C.
Two parameters: specify input PPIN file and name of output SPIN file.
Table
A.
ddi_mei
for
pre-calculated
mutually
exclusive
domain-domain
interactions
ii.
B.
mips2swp: id mapping table (MIPS->SwissProt)
C.
swp2scop: protein domain assignment table (Swissprot: scop families)
output
1.
Summary of the result
2.
SPIN files in the folder specified in spin.properties