This tool performs protein-ligand docking using the rDock program. See http://rdock.sourceforge.net/ for more details about rDock and associated programs.
Inputs
You will need to perform some test dockings to establish suitable values for the score filters. The score is a number with lower values being better. Values can be negative.
Outputs
An SDF file is produced as output. The binding affinity scores are contained within the SDF file.:
1-pyrimethamine rDOCK(R) 3D libRbt.so/2013.1/901 2013/11/27 21 22 0 0 0 0 0 0 0 0999 V2000 -5.1897 17.8912 17.9590 N 0 0 0 0 0 0 -3.9121 17.9973 18.3210 C 0 0 0 0 0 0 -3.2404 19.1465 18.3804 N 0 0 0 0 0 0 -3.8989 20.2829 18.0453 C 0 0 0 0 0 0 -5.2389 20.2802 17.6553 C 0 0 0 0 0 0 -5.8448 19.0235 17.6464 C 0 0 0 0 0 0 -5.9601 21.5065 17.2850 C 0 0 0 0 0 0 -6.2108 22.5074 18.2382 C 0 0 0 0 0 0 -6.8903 23.6771 17.8851 C 0 0 0 0 0 0 -7.3267 23.8556 16.5746 C 0 0 0 0 0 0 -7.0903 22.8744 15.6151 C 0 0 0 0 0 0 -6.4107 21.7051 15.9695 C 0 0 0 0 0 0 -3.2455 16.8582 18.6507 N 0 0 0 0 0 0 -7.1550 18.8446 17.2393 N 0 0 0 0 0 0 -8.1626 25.2957 16.1391 Cl 0 0 0 0 0 0 -2.9891 22.1828 19.5033 C 0 0 0 0 0 0 -3.1112 21.5771 18.1096 C 0 0 0 0 0 0 -2.2766 16.9101 18.9273 H 0 0 0 0 0 0 -3.7237 15.9703 18.6154 H 0 0 0 0 0 0 -7.8809 19.3992 17.6807 H 0 0 0 0 0 0 -7.4159 17.8951 16.9940 H 0 0 0 0 0 0 1 2 2 0 0 0 1 6 1 0 0 0 2 3 1 0 0 0 2 13 1 0 0 0 3 4 2 0 0 0 4 5 1 0 0 0 4 17 1 0 0 0 5 6 2 0 0 0 5 7 1 0 0 0 6 14 1 0 0 0 7 8 2 0 0 0 7 12 1 0 0 0 8 9 1 0 0 0 9 10 2 0 0 0 10 11 1 0 0 0 10 15 1 0 0 0 11 12 2 0 0 0 13 18 1 0 0 0 13 19 1 0 0 0 14 20 1 0 0 0 14 21 1 0 0 0 16 17 1 0 0 0 M END > <CHROM.0> -177.71086620,1.45027861,170.39044546,46.02877151,68.76956623,70.55425150 > <CHROM.1> -81.34718191,-65.90186149,129.45748660,-5.61305786,21.23281353,17.50152835 0.96119776,0.49809360,-3.12917831 > <Rbt.Current_Directory> /home/timbo/github/im/docking-validation/targets/dhfr/expts/vs-simple-rdock > <Rbt.Executable> rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) > <Rbt.Library> libRbt.so (2013.1, Build901 2013/11/27) > <Rbt.Parameter_File> /rDock_2013.1/data/scripts/dock.prm > <Rbt.Receptor> receptor.prm > <SCORE> 0.445364 > <SCORE.INTER> 8.4 > <SCORE.INTER.CONST> 1 > <SCORE.INTER.POLAR> 0 > <SCORE.INTER.REPUL> 0 > <SCORE.INTER.ROT> 3 > <SCORE.INTER.VDW> 0 > <SCORE.INTER.norm> 0.494118 > <SCORE.INTRA> -1.38672 > <SCORE.INTRA.DIHEDRAL> -0.818539 > <SCORE.INTRA.DIHEDRAL.0> 6.01924 > <SCORE.INTRA.POLAR> 0 > <SCORE.INTRA.POLAR.0> 0 > <SCORE.INTRA.REPUL> 0 > <SCORE.INTRA.REPUL.0> 0 > <SCORE.INTRA.VDW> -0.977448 > <SCORE.INTRA.VDW.0> -1.0079 > <SCORE.INTRA.norm> -0.0815716 > <SCORE.RESTR> > <SCORE.RESTR.norm> 0 > <SCORE.SYSTEM> -6.56792 > <SCORE.SYSTEM.CONST> 0 > <SCORE.SYSTEM.DIHEDRAL> 1.50415 > <SCORE.SYSTEM.POLAR> -2.3289 > <SCORE.SYSTEM.VDW> 0.59827 > <SCORE.SYSTEM.norm> -0.386348 > <SCORE.heavy> 17 > <SCORE.norm> 0.0261979 $$$$