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ParDOCK DATA SET

The 226 protein-ligand complexes uploaded here have been prepared in the force field compatible manner. Experimental binding free energies in kcal/mol (EBFE), Predicted binding free energies in kcal/mol (PBFE), Root Mean Square Deviation(RMSD) in Å,name of the protein and the ligand charge of each complex are provided. Click on the PDB ID to download the protein-ligand complex.

      
 S.No.   PDBID          Name  Ligand  Charge    EBFE    PBFE   RMSD
1
1a30
HIV-1 Protease
-2
-5.84
-6.22
1.034
2
1a4k
Antibody FAB
-1
-6.79
-8.1
0.631
3
1a4q
Neuraminidase
-1
-11.77
-8.99
0.346
4
1a4w
Alpha Thrombin
1
-8.13
-9.81
0.440
5
1a9m
HIV-1 Protease
1
-9.41
-11.32
0.700
6
1aaq
HIV-1 Protease
1
-11.45
-11.21
0.271
7
1ac4
Cytochrome C
0
-3.85
-3.92
0.573
8
1acj
Acetyl choline esterase
0
-10.08
-4.55
0.158
9
1acm
Aspartate carbamoyltransferase
-5
-10.31
-7.54
3.103
10
1aco
Aconitase
3
-5.17
-8.32
1.178
11
1ae8
Alpha Thrombin
1
-8.99
-8.26
0.373
12
1aeb
Cytochrome C
0
-4.81
-3.46
2.936
13
1aee
Cytochrome C
0
-3.96
-3.09
1.412
14
1ai4
Pencillin acylase
-1
-3.46
-4.09
0.486
15
1ai5
Pencillin acylase
-1
-5.14
-4.57
0.165
16
1ai6
Pencillin acylase
-1
-5.46
-4.81
0.138
17
1ajn
Pencillin acylase
-1
-3.64
-4.32
0.269
18
1ajp
Pencillin acylase
-1
-3.08
-3.99
0.522
19
1ajv
HIV-1 Protease
0
-10.59
-10.94
0.210
20
1ajx
HIV-1 Protease
0
-10.86
-10.26
0.434
21
1apb
L-arabinose - binding protein
0
-7.94
-4.34
0.367
22
1apt
Penicillopepsin
1
-12.82
-11.43
0.392
23
1apu
Penicillopepsin
0
-10.5
-11.21
0.969
24
1apv
Penicillopepsin
0
-12.35
-11.77
0.569
25
1apw
Penicillopepsin
0
-10.98
-9.61
0.420
26
1b38
Protein-Kinase2
-4
-9.4
-10.67
0.361
27
1b39
Protein-Kinase2
-4
-8.97
-9.87
0.334
28
1b5g
Thrombin
1
-10.91
-10.5
0.297
29
1b6j
HIV-1 Protease
1
-10.76
-12.6
0.371
30
1b6k
HIV-1 Protease
1
-11.88
-13.02
0.313
31
1b6l
HIV-1 Protease
1
-11.28
-11.76
0.382
32
1b6m
HIV-1 Protease
1
-11.41
-11.84
0.494
33
1b9s
Neuraminidase
-1
-4.39
-6.25
3.110
34
1b9t
Neuraminidase
0
-7.04
-8.15
0.243
35
1b9v
Neuraminidase
-1
-5.04
-9.05
0.243
36
1ba8
Thrombin
1
-12.27
-10.26
0.567
37
1bb0
Thrombin
1
-11.4
-10.2
0.465
38
1bdr
HIV-1 Protease
0
-9.07
-10.84
0.306
39
1bil
Renin
0
-12.64
-13.79
0.308
40
1bim
Renin
0
-12.12
-14.02
0.177
41
1bma
Elastase
1
-6.33
-9.98
0.629
42
1bmm
Alpha Thrombin
1
-9.75
-10.06
0.337
43
1bmn
Alpha Thrombin
1
-11.58
-8.68
1.592
44
1bra
Trypsin
1
-2.50
-4.92
2.876
45
1bv7
HIV-1 Protease
0
-12.64
-14.98
0.121
46
1bv9
HIV-1 Protease
0
-12.17
-15.08
0.788
47
1bwa
HIV-1 Protease
0
-10.33
-14.14
0.366
48
1bwb
HIV-1 Protease
0
-10.08
-14.82
0.439
49
1c29
Tryptophan synthase
0
-8.74
-7.37
0.215
50
1c2t
Glycinamide Ribonucleotide Transformaylase
1
-11.07
-11.23
0.290
51
1c5c
Decarboxylase Antibody 21D8
-2
-9.49
-7.78
0.408
52
1c83
Tyrosine Phosphatase 1B
0
-6.59
-7.46
0.225
53
1c85
Tyrosine Phosphatase
-2
-6.41
-8.2
0.957
54
1c86
Tyrosine Phosphatase
-2
-7.09
-8.24
0.404
55
1c87
Tyrosine Phosphatase 1B
-2
-6.59
-8.52
0.185
56
1c88
Tyrosine Phosphatase 1B
-1
-8.86
-8.8
0.159
57
1c8k
Glycogen Phosphorylase
1
-6.79
-7.82
0.522
58
1c9d
Tryptophan synthase
-2
-8.71
-10.19
0.123
59
1cbs
Cellular Retinoic Acid Binding Protein Type II
-1
-9.82
-7.54
0.496
60
1cdg
Cyclodextrin glycosyltransferase
0
-3.3
-2.44
0.331
61
1cf8
Catalytic Antibody 19A4
-1
-8.23
-8.32
0.292
62
1com
Chorismate Mutase
-2
-5.44
-6.22
0.446
63
1cpi
HIV-1 Protease
0
-10.07
-13.14
0.320
64
1cqp
Antigen CD11A
0
-6.61
-6.64
0.324
65
1csc
Citrate synthase
-5
-9.81
-12.04
0.480
66
1ctr
Calmodulin
0
-5.84
-5.46
0.332
67
1ctt
Cytidine deaminase
0
-6.24
-3.93
0.164
68
1cvu
Cyclooxygenase 2
-1
-10.76
-6.94
0.318
69
1cw2
Tyrosine Phosphatase
-2
-8.49
-8.12
0.118
70
1cx2
Cyclooxygenase 2
0
-10.94
-7.16
0.241
71
1cx9
Tryptophan synthase
-2
-9.32
-8.54
0.458
72
1d3d
Alpha thrombin
0
-12.55
-10.78
0.406
73
1d3h
Dihydroorate Dehydrogenase
0
-6.01
-7.46
0.263
74
1d3t
Alpha thrombin
0
-7.78
-9.91
1.006
75
1d4l
HIV-1 Protease
0
-11.92
-12.48
0.322
76
1d4p
Alpha Thrombin
1
-8.59
-8.94
0.402
77
1dg5
Dihydrofolate Reductase
0
-5.53
-6.75
0.241
78
1dhf
Dihydrofolate Reductase
-2
-10.09
-8.77
1.396
79
1die
D - Xylose isomerase
0
-2.92
-2.78
0.160
80
1dmp
HIV-1 Protease
0
-13.03
-11.92
0.344
81
1dog
Glycoamylase 471
0
-5.48
-3.23
0.318
82
1dr1
Dihydrofolate Reductase
1
-7.59
-5.29
0.318
83
1drf
Dihydrofolate Reductase
-2
-10.15
-9.2
0.234
84
1dwb
Alpha Thrombin
1
-3.98
-5.06
0.582
85
1dwc
Alpha Thrombin
0
-10.10
-8.54
0.274
86
1dwd
Alpha Thrombin
1
-11.14
-10.4
0.483
87
1dy9
Protease / Helicase NS3 (P70)
-2
-10.32
-10.29
0.184
88
1c85
Tyrosine Phosphatase
-2
-6.41
-8.2
0.957
89
1eed
Endothiapepsin
-1
-6.54
-8.49
0.818
90
1ela
Elastase
1
-8.66
-8.54
0.432
91
1elb
Elastase
0
-9.75
-7.19
0.316
92
1eld
Elastase
0
-9.13
-8.63
0.187
93
1ele
Elastase
0
-9.33
-8.76
0.848
94
1ent
Endothiapepsin
-1
-9.55
-8
0.878
95
1enu
t-RNA guanine transglycosylase
0
-7.02
-6.02
0.552
96
1epo
Endothiapepsin
0
-10.86
-9.95
0.729
97
1epp
Endothiapepsin
1
-9.77
-10.19
0.270
98
1ets
Epsilon Thrombin
1
-11.62
-9.77
0.682
99
1ett
Epsilon Thrombin
1
-8.44
-8.88
0.374
100
1ezq
Human coagulation factor XA
1
-12.5
-11.24
1.035
101
1f0r
Human coagulation factor XA
0
-10.58
-8.8
0.545
102
1f0t
Trypsin
1
-8.29
-6.92
2.363
103
1f0u
Trypsin
1
-9.89
-8.98
1.599
104
1f3e
t-RNA guanine transglycosylase
0
-9.25
-6.52
0.104
105
1fax
Human coagulation factor XA
0
-10.07
-10.6
0.521
106
1fkg
FK506 Binding Protein
0
-8.81
-6.57
0.256
107
1flr
FAB Fragment
-1
-6.35
-6.25
0.183
108
1g2k
HIV-1 Protease
0
-10.81
-12.13
0.370
109
1ghb
Gamma chymotrypsin
-1
-1.71
-6.13
0.256
110
1gno
HIV-1 Protease
1
-10.57
-10.1
0.290
111
1gpy
Glycogen Phosphorylase
-2
-6.40
-7.07
0.362
112
1hbv
HIV-1 Protease
0
-8.68
-10.91
0.442
113
1hdc
3 - alpha, 20 - beta - hydroxysteroid dehydrogenase
-2
-8.17
-8.03
0.821
114
1hdt
Alpha Thrombin
1
-10.6
-11.87
0.272
115
1hew
Lysozyme
0
-8.18
-8.37
0.501
116
1hge
Hemagglutinin
-1
-3.09
-4.49
0.799
117
1hgh
Hemagglutinin
-1
-3.89
-4.70
0.204
118
1hgi
Hemagglutinin
-1
-3.65
-4.83
0.889
119
1hgj
Hemagglutinin
0
-2.26
-3.65
0.135
120
1hih
HIV-1 Protease
0
-10.97
-11.80
0.204
121
1hii
HIV-2 Protease
0
-9.89
-11.79
0.276
122
1hiv
HIV-1 Protease
0
-12.64
-13.14
0.344
123
1hos
HIV-1 Protease
-1
-11.74
-13.18
0.327
124
1hpo
HIV-1 Protease
0
-11.82
-11.14
0.388
125
1hps
HIV-1 Protease
0
-12.66
-10.94
0.325
126
1hpv
HIV-1 Protease
0
-12.58
-10.83
0.189
127
1hpx
HIV-1 Protease
0
-12.53
-13.18
0.416
128
1hri
Human Rhinovirus
1
-5.91
-7.67
0.208
129
1hrn
Renin
0
-10.94
-11.82
0.216
130
1hsg
HIV-1 Protease
0
-12.93
-12.49
0.347
131
1hsh
HIV-1 Protease
1
-11.69
-12.07
0.332
132
1hte
HIV-1 Protease
0
-7.69
-8.06
0.219
133
1htf
HIV-1 Protease
0
-11.04
-9.99
0.253
134
1htg
HIV-1 Protease
0
-13.21
-12.86
0.440
135
1hvh
HIV-1 Protease
1
-10.81
-12.18
0.454
136
1hvi
HIV-1 Protease
0
-13.74
-15.92
0.208
137
1hvj
HIV-1 Protease
0
-14.26
-15.02
0.206
138
1hvk
HIV-1 Protease
0
-13.80
-15.48
0.523
139
1hvl
HIV-1 Protease
0
-12.28
-14.88
0.319
140
1hvr
HIV-1 Protease
0
-12.97
-12.96
0.195
141
1hxb
HIV-1 Protease
1
-13.48
-12.76
0.287
142
1hxw
HIV-1 Protease
0
-14.54
-14.6
0.327
143
1ida
HIV-2 Protease
0
-11.86
-12.55
0.327
144
1imb
Inositol monophosphatase
-2
-5.73
-3.3
2.930
145
1ivb
Neuraminidase
-1
-4.14
-5.39
1.882
146
1ivf
Neuraminidase
-1
-6.66
-7.62
0.878
147
1k1l
Trypsin
1
-9.56
-7.41
0.374
148
1k1n
Trypsin
0
-8.82
-9.47
0.341
149
1lyb
Cathepsin D
-1
-15.57
-12.36
0.219
150
1mcb
Immunoglobulin
-1
-6.6
-8.5
0.396
151
1mcf
Immunoglobulin
-1
-7.02
-8.54
0.472
152
1mch
Immunoglobulin
-1
-7.02
-8.81
0.284
153
1mcj
Immunoglobulin
0
-5.16
-5.92
0.381
154
1mcs
Immunoglobulin
-1
-6.6
-8.2
0.277
155
1mrk
Alpha trichosanthin
0
-6.17
-5.78
0.389
156
1mtw
Trypsin
1
-10.07
-7.84
1.011
157
1nis
Enolase
-2
-4.08
-6.66
0.188
158
1nnb
Neuraminidase
-1
-5.45
-7.1
0.421
159
1nsc
Neuraminidase
-1
-4.08
-7.85
0.148
160
1ola
Oligopeptide Binding Protein
1
-9.54
-10.16
0.248
161
1pdz
Enolase
-3
-5.03
-5.8
0.381
162
1pgp
6-Phosphogluconate Dehydrogenase
-3
-7.77
-9.15
2.368
163
1phh
p-Hydroxybenzoate Hydroxylase
-1
-3.98
-4.61
0.588
164
1ppc
Trypsin
1
-8.8
-8.46
0.415
165
1pph
Trypsin
1
-8.48
-6.35
1.454
166
1ppk
Penicillopepsin
1
-10.44
-8.91
0.441
167
1ppm
Penicillopepsin
-1
-7.95
-9.74
0.375
168
1pso
pepsin
-1
-14.11
-12.34
0.493
169
1qbr
HIV-1 Protease
0
-14.42
-14.54
0.331
170
1qbt
HIV-1 Protease
0
-14.49
-14.61
0.447
171
1qbu
HIV-1 Protease
0
-13.97
-12.05
0.295
172
1rbp
Retinol Binding Protein
0
-9.17
-7.78
0.233
173
1rgk
Ribonuclease T1
-2
-5.87
-6.82
0.225
174
1rgl
Ribonuclease T1
-2
-6.04
-5.73
2.657
175
1rne
Renin
0
-11.94
-15.1
0.450
176
1snc
Staphylococcal nuclease
-4
-9.25
-11.89
0.228
177
1sre
Streptavidin
-1
-5.45
-6.19
0.266
178
1tlc
Thymidylate Synthase
-2
-10.98
-10.08
0.392
179
1tng
Trypsin
1
-4
-3.93
0.496
180
1tnh
Trypsin
1
-4.59
-4.49
0.379
181
1tni
Trypsin
1
-2.32
-3.74
0.534
182
1tnj
Trypsin
1
-2.67
-3.72
0.316
183
1tnk
Trypsin
1
-2.03
-3.81
0.361
184
1tnl
Trypsin
1
-2.56
-3.56
1.411
185
1tph
Triose phosphate Isomerase
-3
-3.10
-5.21
0.381
186
1tpp
Trypsin
0
-7.95
-6.05
0.212
187
1ulb
Purine Nucleoside Phosphorylase
0
-2.80
-2.84
0.152
188
1uvs
Alpha Thrombin
0
-7.41
-7.53
0.716
189
2abh
Phosphate Binding Protein
-2
-8.88
-7.38
0.571
190
2acs
Aldose Reductase
-3
-2.75
-4.8
0.775
191
2ak3
Adenylate kinase
-2
-5.25
-9.83
0.435
192
2cgr
IGG 2B Fab Fragment
-1
-9.93
-10.56
0.175
193
2cmd
Malate Dehydrogenase
-3
-6.24
-7.77
0.347
194
2er7
Endothiapepsin
-1
-12.27
-13.64
1.034
195
2gbp
D - Galactose D . Glucose binding protein
0
-10.35
-4.74
0.426
196
2ifb
Intestinal Fatty Acid Binding Protein
-1
-7.41
-8.07
0.368
197
2mcp
Immunoglobulin
-1
-7.13
-6.77
0.131
198
2pk4
Human plasminogen
0
-5.88
-2.99
0.331
199
2r04
Rhinovirus 14
0
-8.48
-7.52
0.290
200
2sim
Sialidase
-1
-8.75
-6.8
0.479
201
2upj
HIV-1 Protease
0
-10.14
-10.7
0.493
202
2wea
Penicillopepsin
-1
-8.37
-6.48
0.248
203
2web
Penicillopepsin
-1
-7.03
-9.28
0.371
204
2wec
Penicillopepsin
-1
-6.8
-6.75
0.468
205
2ypi
Triose Phosphate Isomerase
-3
-6.58
-7.19
0.385
206
3er3
Endothiapepsin
1
-9.68
-12.89
0.884
207
3er5
Endothiapepsin
0
-12.35
-14.47
0.394
208
3ptb
Trypsin
1
-6.46
-5.36
0.979
209
4dfr
Dihydrofolate Reductase
-1
-13.23
-11.4
0.301
210
4er2
Endothiapepsin
-1
-11.03
-10.3
0.348
211
4est
Elastase
0
-9.55
-8.08
0.509
212
4hmg
Hemagglutinin
-1
-3.48
-3.97
0.328
213
4phv
HIV-1 Protease
0
-12.47
-12.29
0.381
214
4ts1
Tyrosyl-T / RNA Synthetase
0
-7.64
-4.81
0.199
215
5cna
Agglutinin
0
-2.73
-3.71
0.770
216
5enl
Enolase
-3
-5.24
-6.59
1.050
217
5hvp
HIV-1 Protease
-1
-10.51
-12.9
0.220
218
5tim
Triose Phosphate Isomerase
-2
-3.14
-3.09
0.543
219
6enl
Enolase
-3
-4.14
-5.53
0.506
220
6rnt
Ribonuclease
-2
-8.67
-7.26
0.315
221
6tim
Triose phosphate isomerase
-2
-4.37
-7.59
0.323
222
7dfr
Dihydrofolate Reductase
-2
-10.09
-10.73
0.292
223
7gpb
Glycogen Phosphorylase
-2
-7.53
-7.64
0.943
224
7tim
Triose phosphate isomerase
-2
-7.35
-7.01
0.120
225
8gpb
Glycogen Phosphorylase
-2
-4.91
-5.96
0.530
226
9hvp
HIV-1 Protease
0
-11.38
-13.9
0.515