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binding_affinity

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jglaser commited on
Commit
c066e7c
·
1 Parent(s): 3b0188e

update predictions for D-COID and deepcoy/DEKOIS

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Files changed (6) hide show
  1. .gitattributes +1 -0
  2. data/dcoid_predict.parquet +3 -0
  3. data/deepcoy_dekois_predict.parquet +2 -2
  4. deepcoy_combine.py +7 -0
  5. dekois_targets.txt +84 -0
  6. dude_targets.txt +104 -0
.gitattributes CHANGED
@@ -819,3 +819,4 @@ data/dcoid.parquet filter=lfs diff=lfs merge=lfs -text
819
  data/dcoid_rf2.parquet filter=lfs diff=lfs merge=lfs -text
820
  data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
821
  data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
 
 
819
  data/dcoid_rf2.parquet filter=lfs diff=lfs merge=lfs -text
820
  data/deepcoy_dekois_predict.parquet filter=lfs diff=lfs merge=lfs -text
821
  data/deepcoy_dude_predict.parquet filter=lfs diff=lfs merge=lfs -text
822
+ data/dcoid_predict.parquet filter=lfs diff=lfs merge=lfs -text
data/dcoid_predict.parquet ADDED
@@ -0,0 +1,3 @@
 
 
 
 
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+ version https://git-lfs.github.com/spec/v1
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+ oid sha256:1c7c8522cc43a27d05b68f3828cb5d15d51b655430bb0cac635977fd0258dba1
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+ size 621295
data/deepcoy_dekois_predict.parquet CHANGED
@@ -1,3 +1,3 @@
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  version https://git-lfs.github.com/spec/v1
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- oid sha256:c50a7887a034c148c07ed24a6eba35e04e1319fd9e62a7364fa68ace63fedcab
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- size 3597858
 
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  version https://git-lfs.github.com/spec/v1
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+ oid sha256:c1c7ff872ba4ec0921a146e03edb60505a53ffc936894373b9f4fa1ef953ea44
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+ size 3663538
deepcoy_combine.py CHANGED
@@ -7,6 +7,8 @@ import numpy as np
7
  from Bio.PDB import PDBList
8
  from Bio import SeqIO
9
 
 
 
10
  import warnings
11
 
12
  def get_sequence(pdb_id):
@@ -20,6 +22,9 @@ def get_sequence(pdb_id):
20
  print(e)
21
  pass
22
 
 
 
 
23
  if __name__ == '__main__':
24
  import glob
25
 
@@ -32,6 +37,8 @@ if __name__ == '__main__':
32
  targets = pd.read_csv(sys.argv[1],sep=' ',keep_default_na=False)
33
  for fn in filenames:
34
  df = pd.read_csv(fn,header=None,sep=' ')
 
 
35
  actives = df[0].unique()
36
  decoys = df[1].unique()
37
  smiles += actives.tolist()+decoys.tolist()
 
7
  from Bio.PDB import PDBList
8
  from Bio import SeqIO
9
 
10
+ from rdkit import Chem
11
+
12
  import warnings
13
 
14
  def get_sequence(pdb_id):
 
22
  print(e)
23
  pass
24
 
25
+ def make_canonical(smi):
26
+ return Chem.MolToSmiles(Chem.MolFromSmiles(smi))
27
+
28
  if __name__ == '__main__':
29
  import glob
30
 
 
37
  targets = pd.read_csv(sys.argv[1],sep=' ',keep_default_na=False)
38
  for fn in filenames:
39
  df = pd.read_csv(fn,header=None,sep=' ')
40
+ df[0] = df[0].apply(make_canonical)
41
+ df[1] = df[1].apply(make_canonical)
42
  actives = df[0].unique()
43
  decoys = df[1].unique()
44
  smiles += actives.tolist()+decoys.tolist()
dekois_targets.txt ADDED
@@ -0,0 +1,84 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name pdb
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+ 11betaHSD1 3tfq
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+ 17betaHSD1 3klm
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+ A2A 3eml
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+ ACE 1uze
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+ ACE2 1r4l
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+ ACHE 1eve
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+ ADAM17 3ewj
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+ ADRB2 3ny9
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+ AKT1 3qkl
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+ ALR2 1ah3
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+ AR 1e3g
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+ AURKA 3fdn
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+ AURKB 2vgo
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+ BCL2 2w3l
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+ BRAF 3skc
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+ CATL 3bc3
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+ CDK2 1ckp
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+ COX1 3kk6
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+ COX2 1cx2
21
+ CTSK 3kx1
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+ CYP2A6 1z11
23
+ DHFR 1s3v
24
+ EGFR 1m17
25
+ EPHB4 2vwz
26
+ ERBB2 3pp0
27
+ ER-beta 3oll
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+ FGFR1 1agw
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+ FGFR1 1agw
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+ FKBP1A 2dg3
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+ FXA 1f0r
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+ GBA 2wcg
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+ GR 1nhz
34
+ GSK3B 3i4b
35
+ HDAC2 3max
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+ HDAC8 3sff
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+ HIV1PR 3nu3
38
+ HIV1RT 1s6p
39
+ HMGR 1hw8
40
+ HSP90 1uy6
41
+ IGF1R 3nw7
42
+ INHA 1p44
43
+ ITK 3mj1
44
+ JAK3 3lxl
45
+ KNK1 33lj
46
+ JNK1 3elj
47
+ JNK2 3npc
48
+ JNK3 2b1p
49
+ KIF11 3k5e
50
+ LCK 3mpm
51
+ MDM2 3lbk
52
+ MK2 3kc3
53
+ MMP2 1hov
54
+ NA 1a4g
55
+ P38-alpha 1ouk
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+ PARP-1 3l3m
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+ PDE4b 3frg
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+ PDE5 1xp0
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+ PDK1 2xch
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+ PI3Kg 3dbs
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+ PIM-1 3r04
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+ PIM-2 2iwi
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+ PNP 1b8o
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+ PPARa 2p54
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+ PPARg 1fm9
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+ PR 2w8y
67
+ PRKCQ 1xjd
68
+ PYGL-in 1xoi
69
+ PYGL-out 3dds
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+ QPCT 2afx
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+ ROCK-1 3v8s
72
+ RXR 2p1t
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+ SARS-HCoV 2z94
74
+ SIRT2 1j8f
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+ SRC 2src
76
+ THROMBIN 3rm2
77
+ TIE2 2oo8
78
+ TK 1w4r
79
+ TP 1uou
80
+ TPA 1a5h
81
+ TS 1i00
82
+ uPA 3mhw
83
+ VEGFR1 3hng
84
+ VEGFR2 3c7q
dude_targets.txt ADDED
@@ -0,0 +1,104 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ name pdb
2
+ AA2AR 3eml
3
+ ABL1 2hzi
4
+ ACE 3bkl
5
+ ACES 1e66
6
+ ADA 2e1w
7
+ ADA17 2oi0
8
+ ADRB1 2vt4
9
+ ADRB2 3ny8
10
+ AKT1 3cqw
11
+ AKT2 3d0e
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+ ALDR 2hv5
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+ AMPC 1l2s
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+ ANDR 2am9
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+ AOFB 1s3b
16
+ BACE1 3l5d
17
+ BRAF 3d4q
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+ CAH2 1bcd
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+ CASP3 2cnk
20
+ CDK2 1h00
21
+ COMT 3bwm
22
+ CP2C9 1r9o
23
+ CP3A4 3nxu
24
+ CSF1R 3krj
25
+ CXCR4 3odu
26
+ DEF 1lru
27
+ DHI1 3frj
28
+ DPP4 2i78
29
+ DRD3 3pbl
30
+ DYR 3nxo
31
+ EGFR 2rgp
32
+ ESR1 1sj0
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+ ESR2 2fsz
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+ FA10 3kl6
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+ FA7 1w7x
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+ FABP4 2nnq
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+ FAK1 3bz3
38
+ FGFR1 3c4f
39
+ FKB1A 1j4h
40
+ FNTA 3e37
41
+ FPPS 1zw5
42
+ GCR 3bqd
43
+ GLCM 2v3f
44
+ GRIA2 3kgc
45
+ GRIK1 1vso
46
+ HDAC2 3max
47
+ HDAC8 3f07
48
+ HIVINT 3nf7
49
+ HIVPR 1xl2
50
+ HIVRT 3lan
51
+ HMDH 3ccw
52
+ HS90A 1uyg
53
+ HXK4 3f9m
54
+ IGF1R 2oj9
55
+ INHA 4trj
56
+ INHA_obsolete 2h7l
57
+ ITAL 2ica
58
+ JAK2 3lpb
59
+ KIF11 3cjo
60
+ KIT 3g0e
61
+ KITH 2b8t
62
+ KPCB 2i0e
63
+ LCK 2of2
64
+ LKHA4 3chp
65
+ MAPK2 3m2w
66
+ MCR 2aa2
67
+ MET 3lq8
68
+ MK01 2ojg
69
+ MK10 2zdt
70
+ MK14 2qd9
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+ MMP13 830c
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+ MP2K1 3eqh
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+ NOS1 1qw6
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+ NRAM 1b9v
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+ PA2GA 1kvo
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+ PARP1 3l3m
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+ PDE5A 1udt
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+ PGH1 2oyu
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+ PGH2 3ln1
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+ PLK1 2owb
81
+ PNPH 3bgs
82
+ PPARA 2p54
83
+ PPARD 2znp
84
+ PPARG 2gtk
85
+ PRGR 3kba
86
+ PTN1 2azr
87
+ PUR2 1njs
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+ PYGM 1c8k
89
+ PYRD 1d3g
90
+ RENI 3g6z
91
+ ROCK1 2etr
92
+ RXRA 1mv9
93
+ SAHH 1li4
94
+ SRC 3el8
95
+ TGFR1 3hmm
96
+ THB 1q4x
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+ THRB 1ype
98
+ TRY1 2ayw
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+ TRYB1 2zec
100
+ TYSY 1syn
101
+ UROK 1sqt
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+ VGFR2 2p2i
103
+ WEE1 3biz
104
+ XIAP 3hl5