PostEra

Submission BAR-COM-0f94fc3d

COVID COVID_submissions
#1

Topic automatically created for discussing the designs at:
https://covid.postera.ai/covid/submissions/BAR-COM-0f94fc3d

#2

Adding the formatted text here because otherwise it is unreadable:

Similar approach as previously: https://docs.google.com/document/d/1IZIsCPIoNvEXNFxqCvPKpFO3_Xu_xxR5BqfIj_jTWBE/edit
Data can be found on drive (poses, top scoring cmps): https://drive.google.com/drive/folders/1FzCPYDOHTMLqKxfPJQIP0tIzxeVhHd4L

With the following modifications:

  1. A new query (query2 on drive) was created on the basis of BAR-COM-4e0-39 & TRY-UNI-714-6
  2. A model (fusedmodel_noLig on drive) was created on the basis of those xrays flipping some side chains to allow the docking of molecules going into the pocket that BAR-COM-4e0-39 goes. Two water molecules were kept.
  3. Shape based constraints were used in the docking 3. SPLIF score >0.5 and docking _score <-7.5 was used (SPLIF.sdf.gz on drive)
  4. DISE clustering +visual inspection to increase diversity, selection of 61 compounds (selected2.sdf.gz on drive)
  5. a selection of 5 high scoring compounds on basis of docking score (selected1.sdf.gz on drive)

I’m aware that some cmps have structural alerts, but I think those features we can remove once we have more potent hits (i.e. the Br/N-N linked compounds)
Enamine real ids (please use those):
1 PV-002277046329
2 Z2928955304
3 PV-001867141757
4 Z1892495767
5 PV-001748215410
6 PV-000583972887
7 PV-001480893198
8 Z1168488213
9 Z2844889489
10 Z753334946
11 PV-001763113110
12 Z253767654
13 PV-001822841664
14 PV-001866074687
15 Z1615460427
16 PV-001802409851
17 PV-002420113987
18 Z2872037056
19 PV-001831078512
20 Z1549741431
21 Z1500834591
22 PV-000961429563
23 PV-002220200962
24 PV-001827965241
25 Z872397000
26 Z2196194184
27 PV-001833846204
28 Z2844902552
29 PV-002575024050
30 Z1129286048
31 Z807911692
32 PV-000583972893
33 Z2454425334
34 Z1168475133
35 Z1533000368
36 Z2294336937
37 Z1450263658
38 Z3089567705
39 Z2774676815
40 Z1890058431
41 Z2002942936
42 Z2194312931
43 Z1864147155
44 Z1129288567
45 PV-001871500448
46 Z750350474
47 Z2493443321
48 Z1498001981
49 Z2069076058
50 Z2414553231
51 PV-001801302825
52 Z1129286283
53 PV-002400730800
54 Z1348840233
55 Z3089566497
56 Z2414557205
57 PV-002108321132
58 Z2454423193
59 Z1243866128
60 PV-002596497200
61 Z1870012350
62 PV-001962948064
63 PV-002580993121
64 Z3018666658
65 Z1952750170
66 PV-002352797345