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brianjimenezbrianjimenez
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Using restraints together with membrane protocol
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‎README.md

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@@ -22,7 +22,7 @@ Docking protocols can be found in the `docking` folder. For each of the two prot
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#### 2.1.1. LightDock
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Folder `docking/lightdock` containts data for the different five scenarios: `average`, `blind`, `filtered`, `membrane` and `minimum`.
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Folder `docking/lightdock` containts data for the different six scenarios: `average`, `blind`, `filtered`, `membrane`, `minimum` and `restraints`.
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Each of the scenarios contains for the 18 complexes of the benchmark the following data:
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‎docking/lightdock/restraints/2bs2/lgd_filtered_rank.list

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swarm_85_10.pdb 0.0134228 12.550 34.176 33.090
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swarm_119_8.pdb 0 15.492 62.648 32.672
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swarm_48_10.pdb 0.0536913 13.598 35.524 31.877
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swarm_72_185.pdb 0 19.697 55.053 28.538
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swarm_111_14.pdb 0 16.203 58.353 28.049
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swarm_59_160.pdb 0 17.993 46.112 26.909
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swarm_51_128.pdb 0 16.688 42.273 26.303
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swarm_28_40.pdb 0 18.931 83.957 24.237
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swarm_21_137.pdb 0 23.893 59.467 23.761
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swarm_87_48.pdb 0.00671141 9.732 29.970 22.922
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swarm_102_75.pdb 0.033557 13.053 29.062 22.758
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swarm_76_93.pdb 0 13.697 40.018 21.519
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swarm_113_184.pdb 0 14.867 36.695 15.504
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swarm_18_19.pdb 0.033557 16.953 47.323 3.286

‎docking/lightdock/restraints/2bs2/ligand.pdb

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‎docking/lightdock/restraints/2bs2/lightdock_ligand.pdb

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‎docking/lightdock/restraints/2bs2/lightdock_ligand.pdb.xyz.npy

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‎docking/lightdock/restraints/2bs2/lightdock_receptor_membrane.pdb

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‎docking/lightdock/restraints/2bs2/lightdock_receptor_membrane.pdb.xyz.npy

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‎docking/lightdock/restraints/2bs2/receptor_membrane.pdb

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‎docking/lightdock/restraints/2bs2/restraints.list

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L A.ARG.1071
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L A.ARG.1167
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L A.ARG.1232

‎docking/lightdock/restraints/2bs2/run.sh

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#!/bin/bash
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################
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# You may change these variables according to your needs
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SWARMS=400
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GLOWWORMS=200
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STEPS=100
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CORES=24
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################
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# Setup
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if test -f "restraints.list"; then
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lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane -rst restraints.list
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else
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lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane
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fi
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# Simulation
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lightdock3.py setup.json ${STEPS} -s fastdfire -c ${CORES}
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# Generate predictions in PDB format
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s=`ls -d swarm_* | wc -l`
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swarms=$((s-1))
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for i in $(seq 0 $swarms)
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do
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cd swarm_${i}; lgd_generate_conformations.py ../receptor_membrane.pdb ../ligand.pdb gso_${STEPS}.out ${GLOWWORMS}; cd ..;
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done
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# Cluster per swarm
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for i in $(seq 0 $swarms)
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do
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cd swarm_${i}; lgd_cluster_bsas.py gso_${STEPS}.out; cd ..;
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done
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# Generate ranking
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lgd_rank.py ${swarms} ${STEPS}
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echo "Done."

‎docking/lightdock/restraints/2bs2/setup.json

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{
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"anm_lig": 10,
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"anm_rec": 10,
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"anm_seed": 324324,
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"ftdock_file": null,
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"glowworms": 200,
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"ligand_pdb": "ligand.pdb",
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"active": [
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"A.ARG.1071",
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"A.ARG.1167",
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"A.ARG.1232"
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],
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"membrane": true,
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"noh": true,
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"noxt": true,
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"receptor_pdb": "receptor_membrane.pdb",
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"receptor_restraints": {
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"active": [],
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"blocked": [],
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"passive": []
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},
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"restraints": "restraints.list",
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"starting_points_seed": 324324,
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"swarms": 123,
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"use_anm": false,
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"verbose_parser": false
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}

‎docking/lightdock/restraints/2bs2/top.tgz

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‎docking/lightdock/restraints/2gsk/lgd_filtered_rank.list

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swarm_54_79.pdb 0.0185185 7.465 15.870 49.676
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swarm_47_3.pdb 0.095926 4.285 7.673 48.873
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swarm_54_113.pdb 0 5.973 13.728 38.722
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swarm_53_131.pdb 0 8.940 21.281 36.912
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swarm_48_0.pdb 0 11.557 21.035 33.981
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swarm_41_153.pdb 0.0185185 10.679 21.321 32.883
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swarm_42_168.pdb 0 12.877 25.813 32.002
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swarm_39_8.pdb 0.0555556 6.690 12.495 30.769
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swarm_51_125.pdb 0.37037 3.039 5.620 29.437
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swarm_33_174.pdb 0 12.625 30.628 27.560
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swarm_9_25.pdb 0.0185185 11.902 26.105 26.669
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swarm_46_51.pdb 0.0555556 13.800 30.060 26.647
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swarm_41_40.pdb 0 9.719 21.764 23.710
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swarm_29_40.pdb 0 16.019 35.116 23.509
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swarm_28_46.pdb 0 16.371 27.230 23.253
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swarm_48_187.pdb 0 11.458 24.109 23.129
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swarm_38_121.pdb 0.0185185 9.516 17.726 22.065
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swarm_42_61.pdb 0 9.656 22.833 21.809
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swarm_16_3.pdb 0 14.713 34.060 21.321
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swarm_25_22.pdb 0 15.102 32.398 20.815
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swarm_44_141.pdb 0 12.488 28.715 20.220
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swarm_15_97.pdb 0 14.511 33.105 19.708
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swarm_52_134.pdb 0.0555556 11.743 24.712 19.445
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swarm_14_134.pdb 0 9.370 18.841 19.377
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swarm_35_77.pdb 0.0185185 11.399 25.793 18.983
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swarm_58_196.pdb 0 11.500 27.175 18.925
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swarm_2_116.pdb 0 16.940 38.776 16.710
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swarm_28_107.pdb 0 10.744 23.962 15.798
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swarm_36_165.pdb 0 11.851 28.019 15.415
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swarm_49_24.pdb 0 14.236 28.376 15.105
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swarm_4_185.pdb 0 17.046 39.714 15.008
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swarm_37_128.pdb 0.037037 13.724 24.918 14.579
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swarm_24_96.pdb 0 18.782 40.866 13.738
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swarm_56_181.pdb 0 18.526 46.331 11.956
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swarm_4_47.pdb 0.0185185 14.945 39.598 11.231
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swarm_31_154.pdb 0 15.301 33.286 9.074
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swarm_23_103.pdb 0.0925926 13.591 37.876 7.651
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swarm_14_20.pdb 0 16.370 29.743 4.454

‎docking/lightdock/restraints/2gsk/ligand.pdb

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‎docking/lightdock/restraints/2gsk/lightdock_ligand.pdb

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‎docking/lightdock/restraints/2gsk/lightdock_ligand.pdb.xyz.npy

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‎docking/lightdock/restraints/2gsk/lightdock_receptor_membrane.pdb

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‎docking/lightdock/restraints/2gsk/lightdock_receptor_membrane.pdb.xyz.npy

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‎docking/lightdock/restraints/2gsk/receptor_membrane.pdb

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‎docking/lightdock/restraints/2gsk/restraints.list

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L B.ARG.166
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L B.ARG.204
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L B.ARG.212

‎docking/lightdock/restraints/2gsk/run.sh

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#!/bin/bash
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################
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# You may change these variables according to your needs
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SWARMS=400
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GLOWWORMS=200
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STEPS=100
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CORES=24
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################
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11+
# Setup
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if test -f "restraints.list"; then
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lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane -rst restraints.list
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else
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lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane
16+
fi
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# Simulation
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lightdock3.py setup.json ${STEPS} -s fastdfire -c ${CORES}
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21+
# Generate predictions in PDB format
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s=`ls -d swarm_* | wc -l`
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swarms=$((s-1))
24+
for i in $(seq 0 $swarms)
25+
do
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cd swarm_${i}; lgd_generate_conformations.py ../receptor_membrane.pdb ../ligand.pdb gso_${STEPS}.out ${GLOWWORMS}; cd ..;
27+
done
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# Cluster per swarm
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for i in $(seq 0 $swarms)
31+
do
32+
cd swarm_${i}; lgd_cluster_bsas.py gso_${STEPS}.out; cd ..;
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done
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# Generate ranking
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lgd_rank.py ${swarms} ${STEPS}
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echo "Done."

‎docking/lightdock/restraints/2gsk/setup.json

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{
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"anm_lig": 10,
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"anm_rec": 10,
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"anm_seed": 324324,
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"ftdock_file": null,
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"glowworms": 200,
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"ligand_pdb": "ligand.pdb",
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"ligand_restraints": {
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"active": [
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"B.ARG.204",
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"B.LYS.207",
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"B.ARG.212"
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],
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"blocked": [],
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"passive": []
16+
},
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"membrane": true,
18+
"noh": true,
19+
"noxt": true,
20+
"receptor_pdb": "receptor_membrane.pdb",
21+
"receptor_restraints": {
22+
"active": [],
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"blocked": [],
24+
"passive": []
25+
},
26+
"restraints": "restraints.list",
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"starting_points_seed": 324324,
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"swarms": 59,
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"use_anm": false,
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"verbose_parser": false
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}

‎docking/lightdock/restraints/2gsk/top.tgz

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‎docking/lightdock/restraints/2hdi/lgd_filtered_rank.list

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swarm_9_58.pdb 0.120482 9.409 26.315 44.104
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swarm_95_114.pdb 0.0843373 6.228 23.186 43.136
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swarm_7_182.pdb 0.0361446 7.568 22.438 41.702
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swarm_96_115.pdb 0.0481928 6.253 22.617 39.286
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swarm_15_164.pdb 0 11.253 18.610 38.967
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swarm_37_144.pdb 0 15.558 38.225 38.381
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swarm_33_91.pdb 0.0963855 4.709 15.926 37.461
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swarm_64_100.pdb 0 10.876 29.718 37.297
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swarm_92_81.pdb 0.361446 2.662 9.366 36.622
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swarm_17_143.pdb 0.0843373 8.609 24.834 35.849
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swarm_92_139.pdb 0.0240964 8.998 26.317 35.792
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swarm_91_102.pdb 0.0843373 5.898 23.019 35.694
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swarm_7_149.pdb 0.0481928 8.044 27.493 35.410
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swarm_74_35.pdb 0.228916 4.774 20.327 34.289
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swarm_55_36.pdb 0.0240964 9.785 25.997 33.655
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swarm_13_28.pdb 0.0361446 14.350 39.861 33.313
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swarm_112_176.pdb 0 10.624 24.793 33.012
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swarm_11_85.pdb 0.0240964 10.157 29.385 32.277
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swarm_3_9.pdb 0 10.585 31.766 32.092
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swarm_25_9.pdb 0 10.219 28.758 32.016
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swarm_108_153.pdb 0 17.653 37.392 31.818
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swarm_106_141.pdb 0 10.160 31.329 31.591
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swarm_84_161.pdb 0 10.151 30.559 31.577
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swarm_18_24.pdb 0 12.115 29.952 31.507
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swarm_18_51.pdb 0.204819 6.685 21.214 31.241
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swarm_16_108.pdb 0.0240964 10.076 28.584 30.200
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swarm_30_23.pdb 0.060241 14.876 52.558 29.971
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swarm_113_136.pdb 0 12.612 37.752 29.911
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swarm_33_8.pdb 0.156627 3.322 8.986 29.596
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swarm_92_51.pdb 0.060241 9.201 21.920 29.086
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swarm_39_92.pdb 0.0481928 14.190 47.806 28.912
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swarm_18_107.pdb 0.0120482 9.613 26.578 28.633
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swarm_73_129.pdb 0.0481928 9.607 26.490 28.427
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swarm_8_9.pdb 0.0120482 8.334 27.398 28.089
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swarm_90_189.pdb 0.0120482 9.926 32.704 27.873
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swarm_69_180.pdb 0 17.034 56.703 27.827
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swarm_60_60.pdb 0.060241 11.841 37.132 27.101
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swarm_113_144.pdb 0 9.844 29.546 26.798
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swarm_29_168.pdb 0.0361446 7.382 15.955 26.411
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swarm_60_86.pdb 0 11.790 28.176 25.478
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swarm_52_174.pdb 0.0361446 12.123 45.256 24.908
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swarm_21_118.pdb 0 12.391 33.849 24.835
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swarm_55_60.pdb 0 10.027 31.490 24.701
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swarm_17_178.pdb 0.0361446 10.410 22.890 24.635
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swarm_62_188.pdb 0 15.443 47.587 24.629
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swarm_35_75.pdb 0 15.709 55.476 24.476
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swarm_33_134.pdb 0.0722892 9.639 21.540 24.324
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swarm_90_93.pdb 0 13.223 31.739 23.996
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swarm_96_32.pdb 0.0120482 10.281 30.394 23.656
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swarm_68_155.pdb 0 18.267 54.121 23.585
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swarm_103_27.pdb 0 15.175 44.962 23.371
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swarm_31_118.pdb 0 14.353 38.614 23.271
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swarm_43_182.pdb 0 11.397 18.512 23.248
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swarm_35_139.pdb 0 15.822 55.769 23.107
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swarm_53_79.pdb 0 12.462 43.036 23.035
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swarm_86_113.pdb 0 14.062 35.857 23.018
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swarm_16_166.pdb 0.156627 7.206 27.680 22.951
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swarm_2_84.pdb 0 12.561 44.311 22.677
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swarm_76_159.pdb 0 16.304 56.965 22.629
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swarm_33_46.pdb 0.0120482 8.481 17.489 22.584
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swarm_63_146.pdb 0.0481928 14.349 48.063 22.481
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swarm_47_188.pdb 0 13.217 37.372 22.362
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swarm_51_27.pdb 0 15.309 54.021 22.329
64+
swarm_84_101.pdb 0 11.753 28.993 22.227
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swarm_50_62.pdb 0 18.764 42.857 21.899
66+
swarm_52_27.pdb 0 14.690 49.011 21.874
67+
swarm_90_118.pdb 0.0361446 10.436 29.542 21.783
68+
swarm_68_108.pdb 0 16.732 55.917 21.607
69+
swarm_58_103.pdb 0 14.838 41.058 21.491
70+
swarm_95_13.pdb 0 9.945 30.307 21.466
71+
swarm_59_180.pdb 0 18.049 61.226 21.327
72+
swarm_25_189.pdb 0 11.693 30.115 21.307
73+
swarm_15_57.pdb 0 10.411 25.140 21.198
74+
swarm_86_58.pdb 0 11.661 32.956 21.086
75+
swarm_21_1.pdb 0.0120482 13.411 36.204 21.003
76+
swarm_31_197.pdb 0 14.559 46.043 20.746
77+
swarm_45_167.pdb 0 16.235 52.669 20.704
78+
swarm_73_15.pdb 0.0240964 9.962 23.016 20.687
79+
swarm_38_37.pdb 0 14.912 38.551 20.562
80+
swarm_63_44.pdb 0 12.650 44.873 20.458
81+
swarm_34_146.pdb 0.0361446 14.273 56.159 20.431
82+
swarm_19_178.pdb 0 9.816 33.593 20.429
83+
swarm_4_48.pdb 0 19.044 55.466 20.377
84+
swarm_23_64.pdb 0.0481928 8.859 28.078 20.338
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swarm_20_159.pdb 0 15.456 48.287 20.318
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swarm_89_176.pdb 0 12.806 40.683 20.153
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swarm_29_186.pdb 0.253012 4.459 13.170 20.108
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swarm_42_19.pdb 0.0361446 11.515 35.371 20.048
89+
swarm_110_101.pdb 0.0120482 10.909 44.317 19.993
90+
swarm_45_65.pdb 0 17.950 51.305 19.944
91+
swarm_81_77.pdb 0 16.362 44.730 19.899
92+
swarm_25_82.pdb 0 10.542 24.924 19.868
93+
swarm_63_198.pdb 0.0240964 12.725 41.768 19.865
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swarm_74_189.pdb 0.0722892 4.218 13.895 19.855
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swarm_17_18.pdb 0.108434 6.904 26.478 19.516
96+
swarm_55_65.pdb 0 10.899 26.673 19.349
97+
swarm_34_111.pdb 0 17.398 63.943 19.339
98+
swarm_74_19.pdb 0.0240964 11.142 20.456 19.335
99+
swarm_54_112.pdb 0 15.085 44.917 19.329
100+
swarm_8_176.pdb 0.0843373 3.776 13.115 19.327
101+
swarm_32_25.pdb 0.060241 10.219 28.524 19.248
102+
swarm_113_33.pdb 0 12.158 28.964 19.060
103+
swarm_106_5.pdb 0.0120482 11.618 32.271 19.011
104+
swarm_64_76.pdb 0 13.754 35.002 18.893
105+
swarm_84_46.pdb 0 11.379 29.338 18.672
106+
swarm_29_195.pdb 0 11.748 23.940 18.671
107+
swarm_32_57.pdb 0.0240964 7.794 20.834 18.560
108+
swarm_38_75.pdb 0 12.790 45.242 18.527
109+
swarm_113_123.pdb 0.0120482 11.914 34.657 18.522
110+
swarm_81_196.pdb 0 13.187 34.517 18.243
111+
swarm_39_136.pdb 0 11.798 42.841 18.189
112+
swarm_39_97.pdb 0 14.959 45.722 18.156
113+
swarm_55_26.pdb 0 10.869 29.434 18.058
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swarm_89_45.pdb 0 15.529 36.396 18.048
115+
swarm_53_88.pdb 0 13.244 45.473 17.984
116+
swarm_101_53.pdb 0 15.872 50.738 17.887
117+
swarm_63_137.pdb 0.108434 9.956 39.896 17.625
118+
swarm_72_104.pdb 0.0240964 12.903 41.643 17.197
119+
swarm_3_13.pdb 0 14.387 36.723 17.182
120+
swarm_83_42.pdb 0 14.138 37.703 17.132
121+
swarm_83_10.pdb 0.0120482 7.435 30.974 17.053
122+
swarm_78_53.pdb 0 16.102 52.265 16.891
123+
swarm_97_6.pdb 0 13.301 39.827 16.853
124+
swarm_17_88.pdb 0.0481928 7.403 23.006 16.786
125+
swarm_72_152.pdb 0 11.193 39.818 16.681
126+
swarm_26_15.pdb 0 15.119 52.399 16.642
127+
swarm_109_188.pdb 0 17.008 52.702 16.632
128+
swarm_114_73.pdb 0 18.073 48.734 16.620
129+
swarm_105_119.pdb 0 20.931 56.665 16.554
130+
swarm_90_91.pdb 0 11.411 40.484 16.507
131+
swarm_63_47.pdb 0.0120482 13.455 46.837 16.378
132+
swarm_86_111.pdb 0 12.283 30.341 16.352
133+
swarm_38_176.pdb 0 15.938 49.437 16.297
134+
swarm_19_186.pdb 0 12.618 32.231 16.201
135+
swarm_40_32.pdb 0 12.118 44.446 16.185
136+
swarm_94_108.pdb 0 16.832 50.320 16.091
137+
swarm_95_23.pdb 0 9.827 23.002 16.004
138+
swarm_42_92.pdb 0 13.962 42.289 15.994
139+
swarm_40_128.pdb 0 11.582 41.831 15.978
140+
swarm_96_183.pdb 0 10.955 22.697 15.923
141+
swarm_43_123.pdb 0.0120482 7.426 16.196 15.807
142+
swarm_9_49.pdb 0.0361446 7.746 25.487 15.804
143+
swarm_93_148.pdb 0.0240964 11.631 31.087 15.797
144+
swarm_75_134.pdb 0 14.576 36.031 15.669
145+
swarm_65_39.pdb 0 15.116 35.334 15.594
146+
swarm_71_41.pdb 0 11.088 30.917 15.183
147+
swarm_33_182.pdb 0 10.032 20.066 15.059
148+
swarm_55_180.pdb 0 13.268 34.312 15.042
149+
swarm_24_70.pdb 0 10.531 21.300 15.001
150+
swarm_73_101.pdb 0.0120482 8.984 22.460 14.474
151+
swarm_8_19.pdb 0.0843373 5.484 15.880 14.470
152+
swarm_72_191.pdb 0 13.625 44.081 14.298
153+
swarm_14_19.pdb 0 17.970 49.731 14.042
154+
swarm_84_106.pdb 0.0120482 11.573 30.635 13.896
155+
swarm_106_155.pdb 0 11.288 28.806 13.852
156+
swarm_79_158.pdb 0 17.715 55.108 13.802
157+
swarm_22_172.pdb 0 12.631 40.628 13.666
158+
swarm_22_27.pdb 0 13.953 48.970 13.455
159+
swarm_32_56.pdb 0.0120482 11.610 21.178 13.272
160+
swarm_57_5.pdb 0 12.939 35.876 13.256
161+
swarm_25_123.pdb 0.0120482 11.655 33.966 13.175
162+
swarm_5_51.pdb 0 18.582 53.071 13.102
163+
swarm_68_85.pdb 0 17.223 61.173 13.057
164+
swarm_42_51.pdb 0 14.659 44.179 13.007
165+
swarm_114_130.pdb 0 14.011 36.371 12.888
166+
swarm_110_64.pdb 0 16.910 51.863 12.823
167+
swarm_19_70.pdb 0 13.219 37.417 12.714
168+
swarm_85_73.pdb 0 14.018 35.033 12.501
169+
swarm_82_153.pdb 0 14.751 33.134 12.413
170+
swarm_36_64.pdb 0.0481928 15.048 53.114 11.733
171+
swarm_44_142.pdb 0 16.876 62.920 11.671
172+
swarm_66_111.pdb 0 20.177 55.847 11.293
173+
swarm_81_84.pdb 0 15.172 40.368 10.957
174+
swarm_102_50.pdb 0 15.222 49.728 10.847
175+
swarm_97_174.pdb 0 13.395 40.661 10.625
176+
swarm_65_130.pdb 0 17.598 43.857 10.488
177+
swarm_77_158.pdb 0 18.829 53.729 10.437
178+
swarm_70_28.pdb 0 18.570 58.344 10.125
179+
swarm_78_82.pdb 0 15.086 40.113 9.984
180+
swarm_3_136.pdb 0 11.642 30.676 9.632
181+
swarm_89_118.pdb 0.0120482 15.416 45.828 9.330
182+
swarm_30_133.pdb 0 17.022 53.890 9.319
183+
swarm_94_7.pdb 0 17.334 47.252 8.921
184+
swarm_108_194.pdb 0 18.018 41.910 8.337
185+
swarm_66_100.pdb 0 19.650 51.506 8.310
186+
swarm_54_176.pdb 0 15.204 50.200 7.522
187+
swarm_66_7.pdb 0 18.594 51.606 6.460
188+
swarm_58_152.pdb 0 11.158 37.878 4.899

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