Using restraints together with membrane protocol

README.md

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

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

@@ -0,0 +1,14 @@
+swarm_85_10.pdb	0.0134228	12.550	34.176	33.090
+swarm_119_8.pdb	0	15.492	62.648	32.672
+swarm_48_10.pdb	0.0536913	13.598	35.524	31.877
+swarm_72_185.pdb	0	19.697	55.053	28.538
+swarm_111_14.pdb	0	16.203	58.353	28.049
+swarm_59_160.pdb	0	17.993	46.112	26.909
+swarm_51_128.pdb	0	16.688	42.273	26.303
+swarm_28_40.pdb	0	18.931	83.957	24.237
+swarm_21_137.pdb	0	23.893	59.467	23.761
+swarm_87_48.pdb	0.00671141	9.732	29.970	22.922
+swarm_102_75.pdb	0.033557	13.053	29.062	22.758
+swarm_76_93.pdb	0	13.697	40.018	21.519
+swarm_113_184.pdb	0	14.867	36.695	15.504
+swarm_18_19.pdb	0.033557	16.953	47.323	3.286

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

@@ -0,0 +1,3 @@
+L A.ARG.1071
+L A.ARG.1167
+L A.ARG.1232

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

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+################
+# You may change these variables according to your needs
+SWARMS=400
+GLOWWORMS=200
+STEPS=100
+CORES=24
+################
+
+# Setup
+if test -f "restraints.list"; then
+    lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane -rst restraints.list
+else
+    lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane
+fi
+
+# Simulation
+lightdock3.py setup.json ${STEPS} -s fastdfire -c ${CORES}
+
+# Generate predictions in PDB format
+s=`ls -d swarm_* | wc -l`
+swarms=$((s-1))
+for i in $(seq 0 $swarms)
+  do
+    cd swarm_${i}; lgd_generate_conformations.py ../receptor_membrane.pdb ../ligand.pdb  gso_${STEPS}.out ${GLOWWORMS}; cd ..;
+  done
+
+# Cluster per swarm
+for i in $(seq 0 $swarms)
+  do
+    cd swarm_${i}; lgd_cluster_bsas.py gso_${STEPS}.out; cd ..;
+  done
+
+# Generate ranking
+lgd_rank.py ${swarms} ${STEPS}
+
+echo "Done."

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

@@ -0,0 +1,27 @@
+{
+    "anm_lig": 10,
+    "anm_rec": 10,
+    "anm_seed": 324324,
+    "ftdock_file": null,
+    "glowworms": 200,
+    "ligand_pdb": "ligand.pdb",
+    "active": [
+            "A.ARG.1071",
+            "A.ARG.1167",
+            "A.ARG.1232"
+        ],
+    "membrane": true,
+    "noh": true,
+    "noxt": true,
+    "receptor_pdb": "receptor_membrane.pdb",
+    "receptor_restraints": {
+        "active": [],
+        "blocked": [],
+        "passive": []
+    },
+    "restraints": "restraints.list",
+    "starting_points_seed": 324324,
+    "swarms": 123,
+    "use_anm": false,
+    "verbose_parser": false
+}

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

@@ -0,0 +1,38 @@
+swarm_54_79.pdb	0.0185185	7.465	15.870	49.676
+swarm_47_3.pdb	0.095926	4.285	7.673	48.873
+swarm_54_113.pdb	0	5.973	13.728	38.722
+swarm_53_131.pdb	0	8.940	21.281	36.912
+swarm_48_0.pdb	0	11.557	21.035	33.981
+swarm_41_153.pdb	0.0185185	10.679	21.321	32.883
+swarm_42_168.pdb	0	12.877	25.813	32.002
+swarm_39_8.pdb	0.0555556	6.690	12.495	30.769
+swarm_51_125.pdb	0.37037	3.039	5.620	29.437
+swarm_33_174.pdb	0	12.625	30.628	27.560
+swarm_9_25.pdb	0.0185185	11.902	26.105	26.669
+swarm_46_51.pdb	0.0555556	13.800	30.060	26.647
+swarm_41_40.pdb	0	9.719	21.764	23.710
+swarm_29_40.pdb	0	16.019	35.116	23.509
+swarm_28_46.pdb	0	16.371	27.230	23.253
+swarm_48_187.pdb	0	11.458	24.109	23.129
+swarm_38_121.pdb	0.0185185	9.516	17.726	22.065
+swarm_42_61.pdb	0	9.656	22.833	21.809
+swarm_16_3.pdb	0	14.713	34.060	21.321
+swarm_25_22.pdb	0	15.102	32.398	20.815
+swarm_44_141.pdb	0	12.488	28.715	20.220
+swarm_15_97.pdb	0	14.511	33.105	19.708
+swarm_52_134.pdb	0.0555556	11.743	24.712	19.445
+swarm_14_134.pdb	0	9.370	18.841	19.377
+swarm_35_77.pdb	0.0185185	11.399	25.793	18.983
+swarm_58_196.pdb	0	11.500	27.175	18.925
+swarm_2_116.pdb	0	16.940	38.776	16.710
+swarm_28_107.pdb	0	10.744	23.962	15.798
+swarm_36_165.pdb	0	11.851	28.019	15.415
+swarm_49_24.pdb	0	14.236	28.376	15.105
+swarm_4_185.pdb	0	17.046	39.714	15.008
+swarm_37_128.pdb	0.037037	13.724	24.918	14.579
+swarm_24_96.pdb	0	18.782	40.866	13.738
+swarm_56_181.pdb	0	18.526	46.331	11.956
+swarm_4_47.pdb	0.0185185	14.945	39.598	11.231
+swarm_31_154.pdb	0	15.301	33.286	9.074
+swarm_23_103.pdb	0.0925926	13.591	37.876	7.651
+swarm_14_20.pdb	0	16.370	29.743	4.454

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

@@ -0,0 +1,3 @@
+L B.ARG.166
+L B.ARG.204
+L B.ARG.212

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

@@ -0,0 +1,38 @@
+#!/bin/bash
+
+################
+# You may change these variables according to your needs
+SWARMS=400
+GLOWWORMS=200
+STEPS=100
+CORES=24
+################
+
+# Setup
+if test -f "restraints.list"; then
+    lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane -rst restraints.list
+else
+    lightdock3_setup.py receptor_membrane.pdb ligand.pdb ${SWARMS} ${GLOWWORMS} --noxt --noh -membrane
+fi
+
+# Simulation
+lightdock3.py setup.json ${STEPS} -s fastdfire -c ${CORES}
+
+# Generate predictions in PDB format
+s=`ls -d swarm_* | wc -l`
+swarms=$((s-1))
+for i in $(seq 0 $swarms)
+  do
+    cd swarm_${i}; lgd_generate_conformations.py ../receptor_membrane.pdb ../ligand.pdb  gso_${STEPS}.out ${GLOWWORMS}; cd ..;
+  done
+
+# Cluster per swarm
+for i in $(seq 0 $swarms)
+  do
+    cd swarm_${i}; lgd_cluster_bsas.py gso_${STEPS}.out; cd ..;
+  done
+
+# Generate ranking
+lgd_rank.py ${swarms} ${STEPS}
+
+echo "Done."

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

@@ -0,0 +1,31 @@
+{
+    "anm_lig": 10,
+    "anm_rec": 10,
+    "anm_seed": 324324,
+    "ftdock_file": null,
+    "glowworms": 200,
+    "ligand_pdb": "ligand.pdb",
+    "ligand_restraints": {
+        "active": [
+            "B.ARG.204",
+            "B.LYS.207",
+            "B.ARG.212"
+        ],
+        "blocked": [],
+        "passive": []
+    },
+    "membrane": true,
+    "noh": true,
+    "noxt": true,
+    "receptor_pdb": "receptor_membrane.pdb",
+    "receptor_restraints": {
+        "active": [],
+        "blocked": [],
+        "passive": []
+    },
+    "restraints": "restraints.list",
+    "starting_points_seed": 324324,
+    "swarms": 59,
+    "use_anm": false,
+    "verbose_parser": false
+}

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

@@ -0,0 +1,188 @@
+swarm_9_58.pdb	0.120482	9.409	26.315	44.104
+swarm_95_114.pdb	0.0843373	6.228	23.186	43.136
+swarm_7_182.pdb	0.0361446	7.568	22.438	41.702
+swarm_96_115.pdb	0.0481928	6.253	22.617	39.286
+swarm_15_164.pdb	0	11.253	18.610	38.967
+swarm_37_144.pdb	0	15.558	38.225	38.381
+swarm_33_91.pdb	0.0963855	4.709	15.926	37.461
+swarm_64_100.pdb	0	10.876	29.718	37.297
+swarm_92_81.pdb	0.361446	2.662	9.366	36.622
+swarm_17_143.pdb	0.0843373	8.609	24.834	35.849
+swarm_92_139.pdb	0.0240964	8.998	26.317	35.792
+swarm_91_102.pdb	0.0843373	5.898	23.019	35.694
+swarm_7_149.pdb	0.0481928	8.044	27.493	35.410
+swarm_74_35.pdb	0.228916	4.774	20.327	34.289
+swarm_55_36.pdb	0.0240964	9.785	25.997	33.655
+swarm_13_28.pdb	0.0361446	14.350	39.861	33.313
+swarm_112_176.pdb	0	10.624	24.793	33.012
+swarm_11_85.pdb	0.0240964	10.157	29.385	32.277
+swarm_3_9.pdb	0	10.585	31.766	32.092
+swarm_25_9.pdb	0	10.219	28.758	32.016
+swarm_108_153.pdb	0	17.653	37.392	31.818
+swarm_106_141.pdb	0	10.160	31.329	31.591
+swarm_84_161.pdb	0	10.151	30.559	31.577
+swarm_18_24.pdb	0	12.115	29.952	31.507
+swarm_18_51.pdb	0.204819	6.685	21.214	31.241
+swarm_16_108.pdb	0.0240964	10.076	28.584	30.200
+swarm_30_23.pdb	0.060241	14.876	52.558	29.971
+swarm_113_136.pdb	0	12.612	37.752	29.911
+swarm_33_8.pdb	0.156627	3.322	8.986	29.596
+swarm_92_51.pdb	0.060241	9.201	21.920	29.086
+swarm_39_92.pdb	0.0481928	14.190	47.806	28.912
+swarm_18_107.pdb	0.0120482	9.613	26.578	28.633
+swarm_73_129.pdb	0.0481928	9.607	26.490	28.427
+swarm_8_9.pdb	0.0120482	8.334	27.398	28.089
+swarm_90_189.pdb	0.0120482	9.926	32.704	27.873
+swarm_69_180.pdb	0	17.034	56.703	27.827
+swarm_60_60.pdb	0.060241	11.841	37.132	27.101
+swarm_113_144.pdb	0	9.844	29.546	26.798
+swarm_29_168.pdb	0.0361446	7.382	15.955	26.411
+swarm_60_86.pdb	0	11.790	28.176	25.478
+swarm_52_174.pdb	0.0361446	12.123	45.256	24.908
+swarm_21_118.pdb	0	12.391	33.849	24.835
+swarm_55_60.pdb	0	10.027	31.490	24.701
+swarm_17_178.pdb	0.0361446	10.410	22.890	24.635
+swarm_62_188.pdb	0	15.443	47.587	24.629
+swarm_35_75.pdb	0	15.709	55.476	24.476
+swarm_33_134.pdb	0.0722892	9.639	21.540	24.324
+swarm_90_93.pdb	0	13.223	31.739	23.996
+swarm_96_32.pdb	0.0120482	10.281	30.394	23.656
+swarm_68_155.pdb	0	18.267	54.121	23.585
+swarm_103_27.pdb	0	15.175	44.962	23.371
+swarm_31_118.pdb	0	14.353	38.614	23.271
+swarm_43_182.pdb	0	11.397	18.512	23.248
+swarm_35_139.pdb	0	15.822	55.769	23.107
+swarm_53_79.pdb	0	12.462	43.036	23.035
+swarm_86_113.pdb	0	14.062	35.857	23.018
+swarm_16_166.pdb	0.156627	7.206	27.680	22.951
+swarm_2_84.pdb	0	12.561	44.311	22.677
+swarm_76_159.pdb	0	16.304	56.965	22.629
+swarm_33_46.pdb	0.0120482	8.481	17.489	22.584
+swarm_63_146.pdb	0.0481928	14.349	48.063	22.481
+swarm_47_188.pdb	0	13.217	37.372	22.362
+swarm_51_27.pdb	0	15.309	54.021	22.329
+swarm_84_101.pdb	0	11.753	28.993	22.227
+swarm_50_62.pdb	0	18.764	42.857	21.899
+swarm_52_27.pdb	0	14.690	49.011	21.874
+swarm_90_118.pdb	0.0361446	10.436	29.542	21.783
+swarm_68_108.pdb	0	16.732	55.917	21.607
+swarm_58_103.pdb	0	14.838	41.058	21.491
+swarm_95_13.pdb	0	9.945	30.307	21.466
+swarm_59_180.pdb	0	18.049	61.226	21.327
+swarm_25_189.pdb	0	11.693	30.115	21.307
+swarm_15_57.pdb	0	10.411	25.140	21.198
+swarm_86_58.pdb	0	11.661	32.956	21.086
+swarm_21_1.pdb	0.0120482	13.411	36.204	21.003
+swarm_31_197.pdb	0	14.559	46.043	20.746
+swarm_45_167.pdb	0	16.235	52.669	20.704
+swarm_73_15.pdb	0.0240964	9.962	23.016	20.687
+swarm_38_37.pdb	0	14.912	38.551	20.562
+swarm_63_44.pdb	0	12.650	44.873	20.458
+swarm_34_146.pdb	0.0361446	14.273	56.159	20.431
+swarm_19_178.pdb	0	9.816	33.593	20.429
+swarm_4_48.pdb	0	19.044	55.466	20.377
+swarm_23_64.pdb	0.0481928	8.859	28.078	20.338
+swarm_20_159.pdb	0	15.456	48.287	20.318
+swarm_89_176.pdb	0	12.806	40.683	20.153
+swarm_29_186.pdb	0.253012	4.459	13.170	20.108
+swarm_42_19.pdb	0.0361446	11.515	35.371	20.048
+swarm_110_101.pdb	0.0120482	10.909	44.317	19.993
+swarm_45_65.pdb	0	17.950	51.305	19.944
+swarm_81_77.pdb	0	16.362	44.730	19.899
+swarm_25_82.pdb	0	10.542	24.924	19.868
+swarm_63_198.pdb	0.0240964	12.725	41.768	19.865
+swarm_74_189.pdb	0.0722892	4.218	13.895	19.855
+swarm_17_18.pdb	0.108434	6.904	26.478	19.516
+swarm_55_65.pdb	0	10.899	26.673	19.349
+swarm_34_111.pdb	0	17.398	63.943	19.339
+swarm_74_19.pdb	0.0240964	11.142	20.456	19.335
+swarm_54_112.pdb	0	15.085	44.917	19.329
+swarm_8_176.pdb	0.0843373	3.776	13.115	19.327
+swarm_32_25.pdb	0.060241	10.219	28.524	19.248
+swarm_113_33.pdb	0	12.158	28.964	19.060
+swarm_106_5.pdb	0.0120482	11.618	32.271	19.011
+swarm_64_76.pdb	0	13.754	35.002	18.893
+swarm_84_46.pdb	0	11.379	29.338	18.672
+swarm_29_195.pdb	0	11.748	23.940	18.671
+swarm_32_57.pdb	0.0240964	7.794	20.834	18.560
+swarm_38_75.pdb	0	12.790	45.242	18.527
+swarm_113_123.pdb	0.0120482	11.914	34.657	18.522
+swarm_81_196.pdb	0	13.187	34.517	18.243
+swarm_39_136.pdb	0	11.798	42.841	18.189
+swarm_39_97.pdb	0	14.959	45.722	18.156
+swarm_55_26.pdb	0	10.869	29.434	18.058
+swarm_89_45.pdb	0	15.529	36.396	18.048
+swarm_53_88.pdb	0	13.244	45.473	17.984
+swarm_101_53.pdb	0	15.872	50.738	17.887
+swarm_63_137.pdb	0.108434	9.956	39.896	17.625
+swarm_72_104.pdb	0.0240964	12.903	41.643	17.197
+swarm_3_13.pdb	0	14.387	36.723	17.182
+swarm_83_42.pdb	0	14.138	37.703	17.132
+swarm_83_10.pdb	0.0120482	7.435	30.974	17.053
+swarm_78_53.pdb	0	16.102	52.265	16.891
+swarm_97_6.pdb	0	13.301	39.827	16.853
+swarm_17_88.pdb	0.0481928	7.403	23.006	16.786
+swarm_72_152.pdb	0	11.193	39.818	16.681
+swarm_26_15.pdb	0	15.119	52.399	16.642
+swarm_109_188.pdb	0	17.008	52.702	16.632
+swarm_114_73.pdb	0	18.073	48.734	16.620
+swarm_105_119.pdb	0	20.931	56.665	16.554
+swarm_90_91.pdb	0	11.411	40.484	16.507
+swarm_63_47.pdb	0.0120482	13.455	46.837	16.378
+swarm_86_111.pdb	0	12.283	30.341	16.352
+swarm_38_176.pdb	0	15.938	49.437	16.297
+swarm_19_186.pdb	0	12.618	32.231	16.201
+swarm_40_32.pdb	0	12.118	44.446	16.185
+swarm_94_108.pdb	0	16.832	50.320	16.091
+swarm_95_23.pdb	0	9.827	23.002	16.004
+swarm_42_92.pdb	0	13.962	42.289	15.994
+swarm_40_128.pdb	0	11.582	41.831	15.978
+swarm_96_183.pdb	0	10.955	22.697	15.923
+swarm_43_123.pdb	0.0120482	7.426	16.196	15.807
+swarm_9_49.pdb	0.0361446	7.746	25.487	15.804
+swarm_93_148.pdb	0.0240964	11.631	31.087	15.797
+swarm_75_134.pdb	0	14.576	36.031	15.669
+swarm_65_39.pdb	0	15.116	35.334	15.594
+swarm_71_41.pdb	0	11.088	30.917	15.183
+swarm_33_182.pdb	0	10.032	20.066	15.059
+swarm_55_180.pdb	0	13.268	34.312	15.042
+swarm_24_70.pdb	0	10.531	21.300	15.001
+swarm_73_101.pdb	0.0120482	8.984	22.460	14.474
+swarm_8_19.pdb	0.0843373	5.484	15.880	14.470
+swarm_72_191.pdb	0	13.625	44.081	14.298
+swarm_14_19.pdb	0	17.970	49.731	14.042
+swarm_84_106.pdb	0.0120482	11.573	30.635	13.896
+swarm_106_155.pdb	0	11.288	28.806	13.852
+swarm_79_158.pdb	0	17.715	55.108	13.802
+swarm_22_172.pdb	0	12.631	40.628	13.666
+swarm_22_27.pdb	0	13.953	48.970	13.455
+swarm_32_56.pdb	0.0120482	11.610	21.178	13.272
+swarm_57_5.pdb	0	12.939	35.876	13.256
+swarm_25_123.pdb	0.0120482	11.655	33.966	13.175
+swarm_5_51.pdb	0	18.582	53.071	13.102
+swarm_68_85.pdb	0	17.223	61.173	13.057
+swarm_42_51.pdb	0	14.659	44.179	13.007
+swarm_114_130.pdb	0	14.011	36.371	12.888
+swarm_110_64.pdb	0	16.910	51.863	12.823
+swarm_19_70.pdb	0	13.219	37.417	12.714
+swarm_85_73.pdb	0	14.018	35.033	12.501
+swarm_82_153.pdb	0	14.751	33.134	12.413
+swarm_36_64.pdb	0.0481928	15.048	53.114	11.733
+swarm_44_142.pdb	0	16.876	62.920	11.671
+swarm_66_111.pdb	0	20.177	55.847	11.293
+swarm_81_84.pdb	0	15.172	40.368	10.957
+swarm_102_50.pdb	0	15.222	49.728	10.847
+swarm_97_174.pdb	0	13.395	40.661	10.625
+swarm_65_130.pdb	0	17.598	43.857	10.488
+swarm_77_158.pdb	0	18.829	53.729	10.437
+swarm_70_28.pdb	0	18.570	58.344	10.125
+swarm_78_82.pdb	0	15.086	40.113	9.984
+swarm_3_136.pdb	0	11.642	30.676	9.632
+swarm_89_118.pdb	0.0120482	15.416	45.828	9.330
+swarm_30_133.pdb	0	17.022	53.890	9.319
+swarm_94_7.pdb	0	17.334	47.252	8.921
+swarm_108_194.pdb	0	18.018	41.910	8.337
+swarm_66_100.pdb	0	19.650	51.506	8.310
+swarm_54_176.pdb	0	15.204	50.200	7.522
+swarm_66_7.pdb	0	18.594	51.606	6.460
+swarm_58_152.pdb	0	11.158	37.878	4.899