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Block-wise ablation, manuscript preview tooling, repaired binding sites #4

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1 change: 1 addition & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -169,3 +169,4 @@ scripts/build_natcomms_docx.js
scripts/build_imrad_md.py
scripts/apa_out.json
scripts/figures/
scripts/check_refs.py
213 changes: 111 additions & 102 deletions data/processed/binding_sites.json
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Original file line number Diff line number Diff line change
Expand Up @@ -22,25 +22,25 @@
"uniprot": "O14842"
},
{
"uniprot": "O15552",
"biasdb_name": "FFA2 receptor",
"center_x": 121.3982,
"center_y": 114.1356,
"center_z": 113.9273,
"cocrystal_ligand_n_atoms": null,
"cocrystal_ligand_resname": null,
"confidence": "ok",
"pdb_id": "8T3S",
"structure_source": "pdb",
"method": "consensus",
"notes": "p2rank top + fpocket top agreement = 2.19 \u00c5",
"pdb_id": "9K1D",
"pocket_prediction_agrees": true,
"pocket_prediction_distance_angstroms": 2.188294288573317,
"pocket_score_fpocket": 0.385,
"pocket_score_p2rank": 1.89,
"center_x": 96.4309,
"center_y": 96.1629,
"center_z": 138.8659,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "O15552"
"cocrystal_ligand_resname": null,
"cocrystal_ligand_n_atoms": null,
"pocket_prediction_distance_angstroms": 4.706148663426533,
"pocket_prediction_agrees": true,
"pocket_score_p2rank": 16.99,
"pocket_score_fpocket": 0.01,
"confidence": "ok",
"notes": "p2rank top + fpocket top agreement = 4.71 \u00c5"
},
{
"biasdb_name": "\u03b22-adrenoceptor",
Expand Down Expand Up @@ -253,25 +253,25 @@
"uniprot": "P20309"
},
{
"uniprot": "P21452",
"biasdb_name": "NK2 receptor",
"center_x": 135.1467,
"center_y": 154.615,
"center_z": 106.6592,
"cocrystal_ligand_n_atoms": null,
"cocrystal_ligand_resname": null,
"confidence": "ok",
"method": "consensus",
"notes": "p2rank top + fpocket top agreement = 1.54 \u00c5",
"pdb_id": "7XWO",
"pocket_prediction_agrees": true,
"pocket_prediction_distance_angstroms": 1.5371655525782293,
"pocket_score_fpocket": 0.697,
"pocket_score_p2rank": 34.42,
"structure_source": "pdb",
"method": "primary_only",
"center_x": 114.1459,
"center_y": 103.232,
"center_z": 143.3739,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P21452"
"cocrystal_ligand_resname": null,
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"pocket_prediction_distance_angstroms": 9.265273875342334,
"pocket_prediction_agrees": false,
"pocket_score_p2rank": 35.31,
"pocket_score_fpocket": 0.024,
"confidence": "low_confidence",
"notes": "p2rank top + fpocket top agreement = 9.27 \u00c5"
},
{
"biasdb_name": "S1P1 receptor",
Expand All @@ -295,25 +295,25 @@
"uniprot": "P21453"
},
{
"uniprot": "P21462",
"biasdb_name": "FPR1",
"center_x": 129.6976,
"center_y": 85.7293,
"center_z": 119.9248,
"cocrystal_ligand_n_atoms": null,
"cocrystal_ligand_resname": null,
"confidence": "ok",
"method": "consensus",
"notes": "p2rank top + fpocket top agreement = 0.91 \u00c5",
"pdb_id": "7VFX",
"pocket_prediction_agrees": true,
"pocket_prediction_distance_angstroms": 0.9125193969244265,
"pocket_score_fpocket": 0.507,
"pocket_score_p2rank": 6.55,
"pdb_id": "7EUO",
"structure_source": "pdb",
"method": "primary_only",
"center_x": 108.4012,
"center_y": 115.0815,
"center_z": 76.1135,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P21462"
"cocrystal_ligand_resname": null,
"cocrystal_ligand_n_atoms": null,
"pocket_prediction_distance_angstroms": 10.812407348402004,
"pocket_prediction_agrees": false,
"pocket_score_p2rank": 24.05,
"pocket_score_fpocket": 0.002,
"confidence": "low_confidence",
"notes": "p2rank top + fpocket top agreement = 10.81 \u00c5"
},
{
"biasdb_name": "CB1 receptor",
Expand Down Expand Up @@ -547,25 +547,25 @@
"uniprot": "P29275"
},
{
"uniprot": "P30518",
"biasdb_name": "V2 receptor",
"center_x": 98.2838,
"center_y": 112.9913,
"center_z": 127.3186,
"cocrystal_ligand_n_atoms": null,
"cocrystal_ligand_resname": null,
"confidence": "low_confidence",
"pdb_id": "7DW9",
"structure_source": "pdb",
"method": "primary_only",
"notes": "p2rank top + fpocket top agreement = 13.55 \u00c5",
"pdb_id": "7KH0",
"pocket_prediction_agrees": false,
"pocket_prediction_distance_angstroms": 13.545152622333719,
"pocket_score_fpocket": 0.084,
"pocket_score_p2rank": 1.53,
"center_x": 49.3278,
"center_y": 70.0202,
"center_z": 72.9365,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P30518"
"cocrystal_ligand_resname": null,
"cocrystal_ligand_n_atoms": null,
"pocket_prediction_distance_angstroms": 7.609059392513593,
"pocket_prediction_agrees": false,
"pocket_score_p2rank": 16.23,
"pocket_score_fpocket": 0.144,
"confidence": "low_confidence",
"notes": "p2rank top + fpocket top agreement = 7.61 \u00c5"
},
{
"biasdb_name": "A1 receptor",
Expand Down Expand Up @@ -820,25 +820,25 @@
"uniprot": "P41143"
},
{
"uniprot": "P41145",
"biasdb_name": "\u03ba receptor",
"center_x": 154.11657097226097,
"center_y": 141.57423800513857,
"center_z": 122.21078582037063,
"cocrystal_ligand_n_atoms": 42,
"cocrystal_ligand_resname": "Q6Q",
"confidence": "ok",
"pdb_id": "8DZP",
"structure_source": "pdb",
"method": "cocrystal_ligand",
"notes": "box centered on bounded Q6Q (42 heavy atoms)",
"pdb_id": "7UL2",
"pocket_prediction_agrees": null,
"pocket_prediction_distance_angstroms": null,
"pocket_score_fpocket": null,
"pocket_score_p2rank": null,
"center_x": 129.84212838449787,
"center_y": 120.11083910542149,
"center_z": 93.83938672465663,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P41145"
"cocrystal_ligand_resname": "U99",
"cocrystal_ligand_n_atoms": 31,
"pocket_prediction_distance_angstroms": null,
"pocket_prediction_agrees": null,
"pocket_score_p2rank": null,
"pocket_score_fpocket": null,
"confidence": "ok",
"notes": "box centered on bounded U99 (31 heavy atoms)"
},
{
"biasdb_name": "NOP receptor",
Expand Down Expand Up @@ -904,25 +904,25 @@
"uniprot": "P41595"
},
{
"uniprot": "P41597",
"biasdb_name": "CCR2",
"center_x": 3.083374999463558,
"center_y": -6.391812473535538,
"center_z": -23.6166250705719,
"cocrystal_ligand_n_atoms": 16,
"cocrystal_ligand_resname": "TYS",
"confidence": "ok",
"method": "cocrystal_ligand",
"notes": "box centered on bounded TYS (16 heavy atoms)",
"pdb_id": "7P8X",
"pocket_prediction_agrees": null,
"pocket_prediction_distance_angstroms": null,
"pocket_score_fpocket": null,
"pocket_score_p2rank": null,
"pdb_id": "7XA3",
"structure_source": "pdb",
"method": "consensus",
"center_x": 113.6946,
"center_y": 138.318,
"center_z": 130.1826,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P41597"
"cocrystal_ligand_resname": null,
"cocrystal_ligand_n_atoms": null,
"pocket_prediction_distance_angstroms": 4.824759347532267,
"pocket_prediction_agrees": true,
"pocket_score_p2rank": 23.91,
"pocket_score_fpocket": 0.427,
"confidence": "ok",
"notes": "p2rank top + fpocket top agreement = 4.82 \u00c5"
},
{
"biasdb_name": "MC3 receptor",
Expand Down Expand Up @@ -988,25 +988,25 @@
"uniprot": "P49682"
},
{
"uniprot": "P51681",
"biasdb_name": "CCR5",
"center_x": -3.751437494531274,
"center_y": -11.872749924659729,
"center_z": -18.457124888896942,
"cocrystal_ligand_n_atoms": 16,
"cocrystal_ligand_resname": "TYS",
"confidence": "ok",
"method": "cocrystal_ligand",
"notes": "box centered on bounded TYS (16 heavy atoms)",
"pdb_id": "5YY4",
"pocket_prediction_agrees": null,
"pocket_prediction_distance_angstroms": null,
"pocket_score_fpocket": null,
"pocket_score_p2rank": null,
"pdb_id": "7O7F",
"structure_source": "pdb",
"method": "primary_only",
"center_x": 192.7681,
"center_y": 179.8396,
"center_z": 230.1375,
"size_x": 22.0,
"size_y": 22.0,
"size_z": 22.0,
"structure_source": "pdb",
"uniprot": "P51681"
"cocrystal_ligand_resname": null,
"cocrystal_ligand_n_atoms": null,
"pocket_prediction_distance_angstroms": 13.56752954970882,
"pocket_prediction_agrees": false,
"pocket_score_p2rank": 26.63,
"pocket_score_fpocket": 0.002,
"confidence": "low_confidence",
"notes": "p2rank top + fpocket top agreement = 13.57 \u00c5"
},
{
"biasdb_name": "PAR2",
Expand Down Expand Up @@ -1298,5 +1298,14 @@
"primary_only": 2
},
"receptors": 61
}
},
"repaired_receptors": [
"O15552",
"P21452",
"P21462",
"P30518",
"P41145",
"P41597",
"P51681"
]
}
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