SMAP run

Published: 17 August 2016| Version 2 | DOI: 10.17632/7p38cm7rkf.2
Contributors:
Wouter Haak,
Anita de Waard

Description

The SMAP software is to be used to compare the binding sites of the M.tb proteins structures plus homology models with the binding sites of approved drugs, in an all-against-all manner. We needed 2 runs for proper parameter settings. The second run used a different radius of 5

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Steps to reproduce

Parameters used for this analysis were: #SMAP Properties #Wed Nov 15 10:46:03 PST 2006 MATCH_SECONDARY_STRUCTURE=false MAX_ATOM_SPHERE_RADIUS=5 MIN_PL_ATOM_SPHERE_SIZE=20 LOCAL_SCORE=true MIN_CA_SPHERE_DISTANCE=5.0 MIN_ATOM_SPHERE_DISTANCE=3.0 ASSOCIATE_GRAPH_NODE_FILTER=0.5 MIN_PL_CA_SPHERE_SIZE=5 MAX_CA_SPHERE_RADIUS=7.5 MAX_NUM_PL=5 TIMES_RANDOM_SHUFFLE=0 SCORE_MATRIX=McLACHLAN LIGAND_CONTACT_DISTANCE_CUTOFF=10.0 PRINT_PDB=true SUPER_PDB_OUTPUT_DIR=/Users/danielgarijo/WORK_ISI/smap_v2_0/Output/align_structure_output PRINT_TEMPLATE_LIGAND=false PRINT_QUERY_LIGAND=true PVALUE_CUTOFF=0.0001 TEMPLATE_LIGAND_SITE_ONLY=false #TEMPLATE_LIGAND_ID=NE6,RPT,RFP,RBT,STD QUERY_LIGAND_SITE_ONLY=true #QUERY_LIGAND_ID=