Decoys Part I

  • Last update: 06 March 2017
  • Version: 1.0
2.0/5 rating 1 vote
The complete set of solutions is divided in two files part I and II.
To untar and decompress: tar xvfz results_part1.tgz results_part2.tgz
-----------DIRECTORIES--------------------
/frodock_results/reference_bound -> reference bound strutures
/frodock_results/initial_unbound -> reference unbound structures
/frodock_results/initial_50rot -> unbound initial structures of receptor and ligand with 50 ligand random relative orientations per case.
/frodock_results/results -> Frodock results obtained with all initial structures included in initial_50rot directory
-----------EXAMPLES -------------------
1) if you want to see the results of the 5 first solutions found with the 42nd initial rotated ligand of 1AVX case, enter the command:
>frodockview results/c2_42_1AVX.dat -r 1-5 -e
1 294.72 52.98   355.31  9.67   33.30 112.95 1295.97 2.21  0.80 0.75 0.17
2 121.41 24.99   160.51  17.67 31.30 104.95 1276.58 21.29 6.04 0.00 0.00
3 194.57 105.35 322.19   9.67  35.30 116.95 1274.43 19.23 8.89 0.00 0.00
4 142.19 56.64   165.39  17.67 31.30 102.95 1263.71 25.79 8.58 0.00 0.00
5 242.60 118.29  358.75 11.67 33.30 114.95 1232.21 15.57 7.11 0.00 0.00
-----------------------------   ---------------------   ----------  ------ ----- -----  -----
rotations translations             x y z               score     Lrmsd Irmsd Fnat Fnot
 
To check all the results (10000 docking solutions) just type:
>frodockview results/c2_42_1AVX.dat -e
 
2) if you want to generate the ligand structures for the first 5 solutions:
>frodockview results/c2_42_1AVX.dat -r 1-5 -e -p initial_50rot/E/42_1AVX_l_u.pdb
 
1 294.72 52.98 355.31 9.67 33.30 112.95 1295.97 2.21 0.80 0.75 0.17 => initial_50rot/E/42_1AVX_l_u_1.pdb
2 121.41 24.99 160.51 17.67 31.30 104.95 1276.58 21.29 6.04 0.00 0.00 => initial_50rot/E/42_1AVX_l_u_2.pdb
3 194.57 105.35 322.19 9.67 35.30 116.95 1274.43 19.23 8.89 0.00 0.00 => initial_50rot/E/42_1AVX_l_u_3.pdb
4 142.19 56.64 165.39 17.67 31.30 102.95 1263.71 25.79 8.58 0.00 0.00 => initial_50rot/E/42_1AVX_l_u_4.pdb
5 242.60 118.29 358.75 11.67 33.30 114.95 1232.21 15.57 7.11 0.00 0.00 => initial_50rot/E/42_1AVX_l_u_5.pdb
The corresponding receptor is located in initial_unbound/A/1AHW_r_u.pdb