openbind-hippo

HIPPO notebooks driving the algorithmics for OpenBind phase 0

Instructions

This repository documents the phase 0 fragment merging, compound ordering, elaboration and downsampling done with HIPPO. The procedure roughly follows the FFF_Template

Make sure to do the pre-requisites of the FFF_Template

Starting on a new target/cycle

Use the notebook notebooks/setup_cycle.ipynb to set up for a new target and/or cycle

Merge (compound) stats

a71ev2a-01

Method	Type	Value
XChem Hits	Structures	645
Fragmenstein Pure	Placement Attempts	306598
Fragmenstein Pure	Unique Compounds	168303
Fragmenstein Pure	Compounds w/ Placements	61000
Fragmenstein Pure	Filtered Scaffolds	309
Knitwork Pure	Placement Attempts	1616879
Knitwork Pure	Unique Compounds	89045
Knitwork Pure	Compounds w/ Placements	30000
Knitwork Pure	Filtered Scaffolds	396
Knitwork Impure	Placement Attempts	1870052
Knitwork Impure	Unique Compounds	62735
Knitwork Impure	Compounds w/ Placements	22000
Knitwork Impure	Filtered Scaffolds	813

d68ev3c-01

Method	Type	Value
XChem Hits	Structures	228
Fragmenstein Pure	Placement Attempts	6356
Fragmenstein Pure	Unique Compounds	4829
Fragmenstein Pure	Compounds w/ Placements	1665
Fragmenstein Pure	Filtered Scaffolds	153
Knitwork Pure	Placement Attempts	268518
Knitwork Pure	Unique Compounds	58416
Knitwork Pure	Compounds w/ Placements	19000
Knitwork Pure	Filtered Scaffolds	83
Knitwork Impure	Placement Attempts	285885
Knitwork Impure	Unique Compounds	43631
Knitwork Impure	Compounds w/ Placements	12000
Knitwork Impure	Filtered Scaffolds	109

xx01zvns2b-01

Method	Type	Value
XChem Hits	Structures	337
Fragmenstein Pure	Placement Attempts	98444
Fragmenstein Pure	Unique Compounds	72617
Fragmenstein Pure	Compounds w/ Placements	25000
Fragmenstein Pure	Filtered Scaffolds	2825
Knitwork Pure	Placement Attempts	140608
Knitwork Pure	Unique Compounds	33788
Knitwork Pure	Compounds w/ Placements	15000
Knitwork Pure	Filtered Scaffolds	411
Knitwork Impure	Placement Attempts	146763
Knitwork Impure	Unique Compounds	26774
Knitwork Impure	Compounds w/ Placements	12000
Knitwork Impure	Filtered Scaffolds	378

Pocket stats

d68ev3c

┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
┃ subsite            ┃ num_poses ┃
┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
│ 2 - 7gon/B/201/1   │ 176       │
│ 1 - 7gp9/A/201/1   │ 111       │
│ 4 - 7gp7/A/201/1   │ 61        │
│ 5 - B1120/A/308/1  │ 42        │
│ 3 - 7gpw/B/202/1   │ 17        │
│ 11 - B0517/A/209/1 │ 14        │
│ 10 - 7gq5/A/201/1  │ 8         │
│ 30 - 7gqr/B/201/1  │ 8         │
│ 14 - 7go6/A/201/1  │ 5         │
│ 15 - 7gob/B/201/1  │ 2         │
│ 17 - 7gok/A/201/1  │ 1         │
│ 24 - 7gpz/B/201/1  │ 1         │
│ 25 - 7gq1/A/201/1  │ 1         │
│ 28 - 7gqn/A/201/1  │ 1         │
│ 29 - 7gqn/A/202/1  │ 1         │
└────────────────────┴───────────┘

a71ev2a

┏━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
┃ subsite            ┃ num_poses ┃
┡━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
│ 1 - Active Site    │ 1431      │
│ 6 - A0486/A/147/1  │ 79        │
│ 5 - A3181/A/202/1  │ 73        │
│ 3 - A0541/A/147/1  │ 62        │
│ 2 - A3977/A/202/1  │ 44        │
│ 17 - A1081/A/201/1 │ 30        │
│ 4 - A0525/A/246/1  │ 16        │
└────────────────────┴───────────┘

xx01zvns2b

┏━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━┓
┃ subsite           ┃ num_poses ┃
┡━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━┩
│ 1 - Z4590/B/203/1 │ 3614      │
│ 6 - Z0788/B/302/1 │ 24        │
│ 5 - Z0773/B/401/1 │ 13        │
│ 7 - Z0846/B/301/1 │ 9         │
└───────────────────┴───────────┘