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