Query session database¶
When you interact with protein-detective a session database is created to store the results of your queries. This notebook shows how to query that database.
This notebooks expects that you have run the workflow.ipynb notebook first to create and fill the session database.
In [1]:
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from pathlib import Path
from protein_detective.db import connect
from pathlib import Path
from protein_detective.db import connect
Configure %sql magic to use the session database.
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session_dir = Path("session1")
# connect() is a context manager, to use connection over multiple cells, we cal its enter method directly.
conn = connect(session_dir, read_only=True).__enter__()
%load_ext sql
%sql conn
# %sql does not retain variable set in initialize_db(), so we use Python API for queries that need it.
session_dir = Path("session1")
# connect() is a context manager, to use connection over multiple cells, we cal its enter method directly.
conn = connect(session_dir, read_only=True).__enter__()
%load_ext sql
%sql conn
# %sql does not retain variable set in initialize_db(), so we use Python API for queries that need it.
Loading configurations from /home/verhoes/git/protein-detective/protein-detective/pyproject.toml.
Settings changed:
| Config | value |
|---|---|
| displaylimit | 100 |
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# Paths in the database are relative to the session directory.
# To make full paths, you need to prepend the session directory.
# The session directory is set as a variable in the database.
conn.execute("SELECT getvariable('session_dir')").fetchone()
# Paths in the database are relative to the session directory.
# To make full paths, you need to prepend the session directory.
# The session directory is set as a variable in the database.
conn.execute("SELECT getvariable('session_dir')").fetchone()
Out[3]:
('session1',)
Uniprot search results¶
In [4]:
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%sql SELECT * FROM proteins
%sql SELECT * FROM proteins
Running query in 'DuckDBPyConnection'
Out[4]:
| uniprot_acc | uniprot_id | sequence_length | reviewed | protein_name | taxon_id | taxon_name |
|---|---|---|---|---|---|---|
| A8K0S8 | ME3L2_HUMAN | 358 | True | Putative homeobox protein Meis3-like 2 | 9606 | Homo sapiens |
| O00358 | FOXE1_HUMAN | 373 | True | Forkhead box protein E1 | 9606 | Homo sapiens |
| A0A1B0GVZ6 | MB3LB_HUMAN | 204 | True | Methyl-CpG-binding domain protein 3-like 2B | 9606 | Homo sapiens |
| O00287 | RFXAP_HUMAN | 272 | True | Regulatory factor X-associated protein | 9606 | Homo sapiens |
| O00479 | HMGN4_HUMAN | 90 | True | High mobility group nucleosome-binding domain-containing protein 4 | 9606 | Homo sapiens |
| O00321 | ETV2_HUMAN | 342 | True | ETS translocation variant 2 | 9606 | Homo sapiens |
| O14503 | BHE40_HUMAN | 412 | True | Class E basic helix-loop-helix protein 40 | 9606 | Homo sapiens |
| B2RPK0 | HGB1A_HUMAN | 211 | True | High mobility group protein B1-like 1 | 9606 | Homo sapiens |
| A6NE82 | MB3L3_HUMAN | 208 | True | Methyl-CpG-binding domain protein 3-like 3 | 9606 | Homo sapiens |
| O00571 | DDX3X_HUMAN | 662 | True | ATP-dependent RNA helicase DDX3X | 9606 | Homo sapiens |
| A6NLW8 | DUXA_HUMAN | 204 | True | Double homeobox protein A | 9606 | Homo sapiens |
| A0A2R8Y619 | H2BK1_HUMAN | 122 | True | Histone H2B type 2-K1 | 9606 | Homo sapiens |
| A0A2Z4LIS9 | FXO3B_HUMAN | 290 | True | Forkhead box protein O3B | 9606 | Homo sapiens |
| E9PAV3 | NACAM_HUMAN | 2078 | True | Nascent polypeptide-associated complex subunit alpha, muscle-specific form | 9606 | Homo sapiens |
| A6NN14 | ZN729_HUMAN | 1252 | True | Zinc finger protein 729 | 9606 | Homo sapiens |
| O14497 | ARI1A_HUMAN | 2285 | True | AT-rich interactive domain-containing protein 1A | 9606 | Homo sapiens |
| A6NMT0 | DBX1_HUMAN | 343 | True | Homeobox protein DBX1 | 9606 | Homo sapiens |
| A8MYZ6 | FOXO6_HUMAN | 492 | True | Forkhead box protein O6 | 9606 | Homo sapiens |
| A6NDX5 | ZN840_HUMAN | 716 | True | Zinc finger protein 840 | 9606 | Homo sapiens |
| A8MTQ0 | NOTO_HUMAN | 251 | True | Homeobox protein notochord | 9606 | Homo sapiens |
| O00255 | MEN1_HUMAN | 610 | True | Menin | 9606 | Homo sapiens |
| A6NJ46 | NKX63_HUMAN | 265 | True | Homeobox protein Nkx-6.3 | 9606 | Homo sapiens |
| O14529 | CUX2_HUMAN | 1486 | True | Homeobox protein cut-like 2 | 9606 | Homo sapiens |
| A6NP11 | ZN716_HUMAN | 495 | True | Zinc finger protein 716 | 9606 | Homo sapiens |
| A0A1W2PQ73 | ERFL_HUMAN | 354 | True | ETS domain-containing transcription factor ERF-like | 9606 | Homo sapiens |
| A0A0C5B5G6 | MOTSC_HUMAN | 16 | True | Mitochondrial-derived peptide MOTS-c | 9606 | Homo sapiens |
| B2RD01 | CENP1_HUMAN | 187 | True | Putative CENPB DNA-binding domain-containing protein 1 | 9606 | Homo sapiens |
| A2RRD8 | ZN320_HUMAN | 509 | True | Zinc finger protein 320 | 9606 | Homo sapiens |
| A0A1W2PPK0 | CPHL2_HUMAN | 400 | True | Cytoplasmic polyadenylated homeobox-like protein 2 | 9606 | Homo sapiens |
| O00716 | E2F3_HUMAN | 465 | True | Transcription factor E2F3 | 9606 | Homo sapiens |
| O00327 | BMAL1_HUMAN | 626 | True | Basic helix-loop-helix ARNT-like protein 1 | 9606 | Homo sapiens |
| A6NJT0 | UNC4_HUMAN | 531 | True | Homeobox protein unc-4 homolog | 9606 | Homo sapiens |
| A6NHT5 | HMX3_HUMAN | 357 | True | Homeobox protein HMX3 | 9606 | Homo sapiens |
| B4DXR9 | ZN732_HUMAN | 585 | True | Zinc finger protein 732 | 9606 | Homo sapiens |
| A9YTQ3 | AHRR_HUMAN | 701 | True | Aryl hydrocarbon receptor repressor | 9606 | Homo sapiens |
| O00257 | CBX4_HUMAN | 560 | True | E3 SUMO-protein ligase CBX4 | 9606 | Homo sapiens |
| A6NHJ4 | ZN860_HUMAN | 632 | True | Zinc finger protein 860 | 9606 | Homo sapiens |
| A0A1W2PQL4 | ZN722_HUMAN | 384 | True | Zinc finger protein 722 | 9606 | Homo sapiens |
| A8MTY0 | ZN724_HUMAN | 619 | True | Zinc finger protein 724 | 9606 | Homo sapiens |
| O14646 | CHD1_HUMAN | 1710 | True | Chromodomain-helicase-DNA-binding protein 1 | 9606 | Homo sapiens |
| O00712 | NFIB_HUMAN | 420 | True | Nuclear factor 1 B-type | 9606 | Homo sapiens |
| A6NJG6 | ARGFX_HUMAN | 315 | True | Arginine-fifty homeobox | 9606 | Homo sapiens |
| A8MXY4 | ZNF99_HUMAN | 864 | True | Zinc finger protein 99 | 9606 | Homo sapiens |
| A8MPP1 | D11L8_HUMAN | 907 | True | Putative ATP-dependent DNA helicase DDX11-like protein 8 | 9606 | Homo sapiens |
| A0A0U1RQI7 | KLF18_HUMAN | 1052 | True | Kruppel-like factor 18 | 9606 | Homo sapiens |
| A6NGD5 | ZSA5C_HUMAN | 496 | True | Zinc finger and SCAN domain-containing protein 5C | 9606 | Homo sapiens |
| A6NJL1 | ZSA5B_HUMAN | 495 | True | Zinc finger and SCAN domain-containing protein 5B | 9606 | Homo sapiens |
| O00470 | MEIS1_HUMAN | 390 | True | Homeobox protein Meis1 | 9606 | Homo sapiens |
| O00110 | OVOL3_HUMAN | 190 | True | Putative transcription factor ovo-like protein 3 | 9606 | Homo sapiens |
| A6NKF2 | ARI3C_HUMAN | 412 | True | AT-rich interactive domain-containing protein 3C | 9606 | Homo sapiens |
| O00482 | NR5A2_HUMAN | 541 | True | Nuclear receptor subfamily 5 group A member 2 | 9606 | Homo sapiens |
| A0A1B0GWH4 | HSFX3_HUMAN | 333 | True | Heat shock transcription factor, X-linked member 3 | 9606 | Homo sapiens |
| A0A1B0GTS1 | HSFX4_HUMAN | 333 | True | Heat shock transcription factor, X-linked member 4 | 9606 | Homo sapiens |
| E9PGG2 | ANHX_HUMAN | 379 | True | Anomalous homeobox protein | 9606 | Homo sapiens |
| A8MUZ8 | Z705G_HUMAN | 300 | True | Putative zinc finger protein 705G | 9606 | Homo sapiens |
| A8MZ59 | LEUTX_HUMAN | 198 | True | Paired-like homeodomain transcription factor LEUTX | 9606 | Homo sapiens |
| A0A1W2PPM1 | CPHXL_HUMAN | 405 | True | Cytoplasmic polyadenylated homeobox-like protein | 9606 | Homo sapiens |
| A6NNF4 | ZN726_HUMAN | 616 | True | Zinc finger protein 726 | 9606 | Homo sapiens |
| O14628 | ZN195_HUMAN | 629 | True | Zinc finger protein 195 | 9606 | Homo sapiens |
| A8K830 | OCAT2_HUMAN | 251 | True | POU class 2 homeobox associating factor 3 | 9606 | Homo sapiens |
| A8K8V0 | ZN785_HUMAN | 405 | True | Zinc finger protein 785 | 9606 | Homo sapiens |
| B4DU55 | ZN879_HUMAN | 563 | True | Zinc finger protein 879 | 9606 | Homo sapiens |
| A8MUV8 | ZN727_HUMAN | 499 | True | Zinc finger protein 727 | 9606 | Homo sapiens |
| C9JSJ3 | MEIOS_HUMAN | 638 | True | Meiosis initiator protein | 9606 | Homo sapiens |
| A8MWA4 | Z705E_HUMAN | 300 | True | Putative zinc finger protein 705EP | 9606 | Homo sapiens |
| O00570 | SOX1_HUMAN | 391 | True | Transcription factor SOX-1 | 9606 | Homo sapiens |
| A6NNA5 | DRGX_HUMAN | 263 | True | Dorsal root ganglia homeobox protein | 9606 | Homo sapiens |
| A8MT69 | CENPX_HUMAN | 81 | True | Centromere protein X | 9606 | Homo sapiens |
| O14593 | RFXK_HUMAN | 260 | True | DNA-binding protein RFXANK | 9606 | Homo sapiens |
| A1A519 | F170A_HUMAN | 330 | True | Protein FAM170A | 9606 | Homo sapiens |
| A6NK75 | ZNF98_HUMAN | 572 | True | Zinc finger protein 98 | 9606 | Homo sapiens |
| A6NFD8 | HELT_HUMAN | 242 | True | Hairy and enhancer of split-related protein HELT | 9606 | Homo sapiens |
| A6NM28 | ZFP92_HUMAN | 416 | True | Zinc finger protein 92 homolog | 9606 | Homo sapiens |
| A6NK53 | ZN233_HUMAN | 670 | True | Zinc finger protein 233 | 9606 | Homo sapiens |
| A6NCS4 | NKX26_HUMAN | 301 | True | Homeobox protein Nkx-2.6 | 9606 | Homo sapiens |
| A6NDZ8 | MB3L4_HUMAN | 208 | True | Methyl-CpG-binding domain protein 3-like 4 | 9606 | Homo sapiens |
| A8MQ14 | ZN850_HUMAN | 1090 | True | Zinc finger protein 850 | 9606 | Homo sapiens |
| A0A087WUV0 | ZN892_HUMAN | 522 | True | Zinc finger protein 892 | 9606 | Homo sapiens |
| A2RU54 | HMX2_HUMAN | 273 | True | Homeobox protein HMX2 | 9606 | Homo sapiens |
| A6NDR6 | ME3L1_HUMAN | 274 | True | Putative homeobox protein Meis3-like 1 | 9606 | Homo sapiens |
| A6NI15 | MSGN1_HUMAN | 193 | True | Mesogenin-1 | 9606 | Homo sapiens |
| A6NFI3 | ZN316_HUMAN | 1004 | True | Zinc finger protein 316 | 9606 | Homo sapiens |
| A0A1W2PPF3 | DUXB_HUMAN | 345 | True | Double homeobox protein B | 9606 | Homo sapiens |
| O00409 | FOXN3_HUMAN | 490 | True | Forkhead box protein N3 | 9606 | Homo sapiens |
| A6NJ08 | MB3L5_HUMAN | 208 | True | Methyl-CpG-binding domain protein 3-like 5 | 9606 | Homo sapiens |
| A0A5F9ZHS7 | NFILZ_HUMAN | 289 | True | NFIL3 like protein | 9606 | Homo sapiens |
| A1YPR0 | ZBT7C_HUMAN | 619 | True | Zinc finger and BTB domain-containing protein 7C | 9606 | Homo sapiens |
| B2RXF5 | ZBT42_HUMAN | 422 | True | Zinc finger and BTB domain-containing protein 42 | 9606 | Homo sapiens |
| O14627 | CDX4_HUMAN | 284 | True | Homeobox protein CDX-4 | 9606 | Homo sapiens |
| A3KN83 | SBNO1_HUMAN | 1393 | True | Protein strawberry notch homolog 1 | 9606 | Homo sapiens |
| A8MTJ6 | FOXI3_HUMAN | 420 | True | Forkhead box protein I3 | 9606 | Homo sapiens |
| A6NFQ7 | DPRX_HUMAN | 191 | True | Divergent paired-related homeobox | 9606 | Homo sapiens |
| A0A3B3IU63 | H2AL3_HUMAN | 148 | True | Histone H2A-like 3 | 9606 | Homo sapiens |
| B1APH4 | ZN487_HUMAN | 207 | True | Zinc finger protein 487 | 9606 | Homo sapiens |
| O00268 | TAF4_HUMAN | 1085 | True | Transcription initiation factor TFIID subunit 4 | 9606 | Homo sapiens |
| C9JN71 | ZN878_HUMAN | 531 | True | Zinc finger protein 878 | 9606 | Homo sapiens |
| A8MT65 | ZN891_HUMAN | 544 | True | Zinc finger protein 891 | 9606 | Homo sapiens |
| B4DX44 | ZN736_HUMAN | 427 | True | Zinc finger protein 736 | 9606 | Homo sapiens |
| A0A1W2PRP0 | FOXL3_HUMAN | 233 | True | Forkhead box protein L3 | 9606 | Homo sapiens |
| E7ETH6 | Z587B_HUMAN | 402 | True | Zinc finger protein 587B | 9606 | Homo sapiens |
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%sql SELECT * FROM pdbs
%sql SELECT * FROM pdbs
Running query in 'DuckDBPyConnection'
Out[5]:
| pdb_id | method | resolution | mmcif_file |
|---|---|---|---|
| 1H3O | X-Ray_Crystallography | 2.299999952316284 | downloads/pdbe/1h3o.cif.gz |
| 2P6V | X-Ray_Crystallography | 2.0 | downloads/pdbe/2p6v.cif.gz |
| 6LTH | Electron_Microscopy | 3.0 | downloads/pdbe/6lth.cif.gz |
| 6LTJ | Electron_Microscopy | 3.700000047683716 | downloads/pdbe/6ltj.cif.gz |
| 1RYU | NMR_Spectroscopy | None | downloads/pdbe/1ryu.cif.gz |
| 1WH6 | NMR_Spectroscopy | None | downloads/pdbe/1wh6.cif.gz |
| 1WH8 | NMR_Spectroscopy | None | downloads/pdbe/1wh8.cif.gz |
| 1X2L | NMR_Spectroscopy | None | downloads/pdbe/1x2l.cif.gz |
| 3TX7 | X-Ray_Crystallography | 2.759999990463257 | downloads/pdbe/3tx7.cif.gz |
| 4DOS | X-Ray_Crystallography | 2.0 | downloads/pdbe/4dos.cif.gz |
| 5UNJ | X-Ray_Crystallography | 1.9600000381469727 | downloads/pdbe/5unj.cif.gz |
| 4PLE | X-Ray_Crystallography | 1.75 | downloads/pdbe/4ple.cif.gz |
| 4DOR | X-Ray_Crystallography | 1.899999976158142 | downloads/pdbe/4dor.cif.gz |
| 5L11 | X-Ray_Crystallography | 1.850000023841858 | downloads/pdbe/5l11.cif.gz |
| 3PLZ | X-Ray_Crystallography | 1.75 | downloads/pdbe/3plz.cif.gz |
| 4ONI | X-Ray_Crystallography | 1.7999999523162842 | downloads/pdbe/4oni.cif.gz |
| 1ZDU | X-Ray_Crystallography | 2.5 | downloads/pdbe/1zdu.cif.gz |
| 1YUC | X-Ray_Crystallography | 1.899999976158142 | downloads/pdbe/1yuc.cif.gz |
| 4PLD | X-Ray_Crystallography | 1.75 | downloads/pdbe/4pld.cif.gz |
| 5L0M | X-Ray_Crystallography | 2.200000047683716 | downloads/pdbe/5l0m.cif.gz |
| 5SYZ | X-Ray_Crystallography | 1.9299999475479126 | downloads/pdbe/5syz.cif.gz |
| 4IS8 | X-Ray_Crystallography | 2.7799999713897705 | downloads/pdbe/4is8.cif.gz |
| 2A66 | X-Ray_Crystallography | 2.200000047683716 | downloads/pdbe/2a66.cif.gz |
| 1YOK | X-Ray_Crystallography | 2.5 | downloads/pdbe/1yok.cif.gz |
| 4RWV | X-Ray_Crystallography | 1.8600000143051147 | downloads/pdbe/4rwv.cif.gz |
| 5AFW | X-Ray_Crystallography | 1.600000023841858 | downloads/pdbe/5afw.cif.gz |
| 2B2Y | X-Ray_Crystallography | 2.3499999046325684 | downloads/pdbe/2b2y.cif.gz |
| 2B2U | X-Ray_Crystallography | 2.950000047683716 | downloads/pdbe/2b2u.cif.gz |
| 2N39 | NMR_Spectroscopy | None | downloads/pdbe/2n39.cif.gz |
| 4O42 | X-Ray_Crystallography | 1.8700000047683716 | downloads/pdbe/4o42.cif.gz |
| 4B4C | X-Ray_Crystallography | 1.6200000047683716 | downloads/pdbe/4b4c.cif.gz |
| 2B2V | X-Ray_Crystallography | 2.6500000953674316 | downloads/pdbe/2b2v.cif.gz |
| 2B2T | X-Ray_Crystallography | 2.450000047683716 | downloads/pdbe/2b2t.cif.gz |
| 4NW2 | X-Ray_Crystallography | 1.899999976158142 | downloads/pdbe/4nw2.cif.gz |
| 2B2W | X-Ray_Crystallography | 2.4000000953674316 | downloads/pdbe/2b2w.cif.gz |
| 2JGN | X-Ray_Crystallography | 1.909999966621399 | downloads/pdbe/2jgn.cif.gz |
| 4PXA | X-Ray_Crystallography | 3.200000047683716 | downloads/pdbe/4pxa.cif.gz |
| 5E7J | X-Ray_Crystallography | 2.2300000190734863 | downloads/pdbe/5e7j.cif.gz |
| 4O2E | X-Ray_Crystallography | 1.9800000190734863 | downloads/pdbe/4o2e.cif.gz |
| 3JRV | X-Ray_Crystallography | 1.600000023841858 | downloads/pdbe/3jrv.cif.gz |
| 2I4I | X-Ray_Crystallography | 2.200000047683716 | downloads/pdbe/2i4i.cif.gz |
| 5E7M | X-Ray_Crystallography | 2.299999952316284 | downloads/pdbe/5e7m.cif.gz |
| 4O2C | X-Ray_Crystallography | 1.7999999523162842 | downloads/pdbe/4o2c.cif.gz |
| 6CZ5 | X-Ray_Crystallography | 3.0 | downloads/pdbe/6cz5.cif.gz |
| 4PX9 | X-Ray_Crystallography | 2.309999942779541 | downloads/pdbe/4px9.cif.gz |
| 5E7I | X-Ray_Crystallography | 2.2200000286102295 | downloads/pdbe/5e7i.cif.gz |
| 4O2F | X-Ray_Crystallography | 1.899999976158142 | downloads/pdbe/4o2f.cif.gz |
| 5EPL | X-Ray_Crystallography | 1.809999942779541 | downloads/pdbe/5epl.cif.gz |
| 3I8Z | X-Ray_Crystallography | 1.5099999904632568 | downloads/pdbe/3i8z.cif.gz |
| 2K28 | NMR_Spectroscopy | None | downloads/pdbe/2k28.cif.gz |
| 2KW3 | NMR_Spectroscopy | None | downloads/pdbe/2kw3.cif.gz |
| 4OG7 | X-Ray_Crystallography | 2.0799999237060547 | downloads/pdbe/4og7.cif.gz |
| 3U85 | X-Ray_Crystallography | 3.0 | downloads/pdbe/3u85.cif.gz |
| 3U84 | X-Ray_Crystallography | 2.5 | downloads/pdbe/3u84.cif.gz |
| 4GQ6 | X-Ray_Crystallography | 1.5499999523162842 | downloads/pdbe/4gq6.cif.gz |
| 4GQ3 | X-Ray_Crystallography | 1.559999942779541 | downloads/pdbe/4gq3.cif.gz |
| 6BXH | X-Ray_Crystallography | 2.440000057220459 | downloads/pdbe/6bxh.cif.gz |
| 4X5Y | X-Ray_Crystallography | 1.590000033378601 | downloads/pdbe/4x5y.cif.gz |
| 5DDE | X-Ray_Crystallography | 1.7799999713897705 | downloads/pdbe/5dde.cif.gz |
| 3U86 | X-Ray_Crystallography | 2.8399999141693115 | downloads/pdbe/3u86.cif.gz |
| 5DDA | X-Ray_Crystallography | 1.8300000429153442 | downloads/pdbe/5dda.cif.gz |
| 4OG4 | X-Ray_Crystallography | 1.4500000476837158 | downloads/pdbe/4og4.cif.gz |
| 5DB1 | X-Ray_Crystallography | 1.8600000143051147 | downloads/pdbe/5db1.cif.gz |
| 4GPQ | X-Ray_Crystallography | 1.4600000381469727 | downloads/pdbe/4gpq.cif.gz |
| 5DB2 | X-Ray_Crystallography | 1.5399999618530273 | downloads/pdbe/5db2.cif.gz |
| 5DDC | X-Ray_Crystallography | 1.6200000047683716 | downloads/pdbe/5ddc.cif.gz |
| 6B41 | X-Ray_Crystallography | 2.609999895095825 | downloads/pdbe/6b41.cif.gz |
| 4X5Z | X-Ray_Crystallography | 1.8600000143051147 | downloads/pdbe/4x5z.cif.gz |
| 6E1A | X-Ray_Crystallography | 3.0999999046325684 | downloads/pdbe/6e1a.cif.gz |
| 5DD9 | X-Ray_Crystallography | 1.6200000047683716 | downloads/pdbe/5dd9.cif.gz |
| 4I80 | X-Ray_Crystallography | 3.0999999046325684 | downloads/pdbe/4i80.cif.gz |
| 4OG5 | X-Ray_Crystallography | 1.6299999952316284 | downloads/pdbe/4og5.cif.gz |
| 4OG8 | X-Ray_Crystallography | 1.5299999713897705 | downloads/pdbe/4og8.cif.gz |
| 6BXY | X-Ray_Crystallography | 1.8200000524520874 | downloads/pdbe/6bxy.cif.gz |
| 5DDF | X-Ray_Crystallography | 1.659999966621399 | downloads/pdbe/5ddf.cif.gz |
| 5DB3 | X-Ray_Crystallography | 1.7100000381469727 | downloads/pdbe/5db3.cif.gz |
| 6BY8 | X-Ray_Crystallography | 1.899999976158142 | downloads/pdbe/6by8.cif.gz |
| 5DB0 | X-Ray_Crystallography | 1.5 | downloads/pdbe/5db0.cif.gz |
| 4OG6 | X-Ray_Crystallography | 1.4900000095367432 | downloads/pdbe/4og6.cif.gz |
| 5DDD | X-Ray_Crystallography | 2.140000104904175 | downloads/pdbe/5ddd.cif.gz |
| 5DDB | X-Ray_Crystallography | 1.5399999618530273 | downloads/pdbe/5ddb.cif.gz |
| 4GQ4 | X-Ray_Crystallography | 1.2699999809265137 | downloads/pdbe/4gq4.cif.gz |
| 4OG3 | X-Ray_Crystallography | 2.009999990463257 | downloads/pdbe/4og3.cif.gz |
| 3U88 | X-Ray_Crystallography | 3.0 | downloads/pdbe/3u88.cif.gz |
| 3V30 | X-Ray_Crystallography | 1.5700000524520874 | downloads/pdbe/3v30.cif.gz |
| 3UXG | X-Ray_Crystallography | 1.850000023841858 | downloads/pdbe/3uxg.cif.gz |
| 6MEW | X-Ray_Crystallography | 1.7799999713897705 | downloads/pdbe/6mew.cif.gz |
| 4DRB | X-Ray_Crystallography | 2.630000114440918 | downloads/pdbe/4drb.cif.gz |
| 4NE3 | X-Ray_Crystallography | 1.7999999523162842 | downloads/pdbe/4ne3.cif.gz |
| 4E45 | X-Ray_Crystallography | 2.0 | downloads/pdbe/4e45.cif.gz |
| 4NE6 | X-Ray_Crystallography | 2.0999999046325684 | downloads/pdbe/4ne6.cif.gz |
| 4NDY | X-Ray_Crystallography | 7.0 | downloads/pdbe/4ndy.cif.gz |
| 4NE5 | X-Ray_Crystallography | 2.5 | downloads/pdbe/4ne5.cif.gz |
| 4DRA | X-Ray_Crystallography | 2.4100000858306885 | downloads/pdbe/4dra.cif.gz |
| 4E44 | X-Ray_Crystallography | 2.0999999046325684 | downloads/pdbe/4e44.cif.gz |
| 4NE1 | X-Ray_Crystallography | 6.5 | downloads/pdbe/4ne1.cif.gz |
| 4H10 | X-Ray_Crystallography | 2.4000000953674316 | downloads/pdbe/4h10.cif.gz |
| 4XRS | X-Ray_Crystallography | 3.5 | downloads/pdbe/4xrs.cif.gz |
| 5EGO | X-Ray_Crystallography | 2.5399999618530273 | downloads/pdbe/5ego.cif.gz |
| 5Y7Y | X-Ray_Crystallography | 2.4000000953674316 | downloads/pdbe/5y7y.cif.gz |
In [6]:
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%sql SELECT * FROM proteins_pdbs
%sql SELECT * FROM proteins_pdbs
Running query in 'DuckDBPyConnection'
Out[6]:
| uniprot_acc | pdb_id | uniprot_chains | chain |
|---|---|---|---|
| O00268 | 1H3O | A/C=872-945 | A |
| O00268 | 2P6V | A=575-688 | A |
| O14497 | 6LTH | L=1-2285 | L |
| O14497 | 6LTJ | L=991-2285 | L |
| O14497 | 1RYU | A=1000-1119 | A |
| O14529 | 1WH6 | A=887-974 | A |
| O14529 | 1WH8 | A=1028-1125 | A |
| O14529 | 1X2L | A=544-631 | A |
| O00482 | 3TX7 | B=191-541 | B |
| O00482 | 4DOS | A=299-538 | A |
| O00482 | 5UNJ | A=299-541 | A |
| O00482 | 4PLE | A/C/E/G=301-541 | A |
| O00482 | 4DOR | A/B=290-541 | A |
| O00482 | 5L11 | A=299-541 | A |
| O00482 | 3PLZ | A/B=300-541 | A |
| O00482 | 4ONI | A/B=291-541 | A |
| O00482 | 1ZDU | A=297-541 | A |
| O00482 | 1YUC | A/B=290-541 | A |
| O00482 | 4PLD | A=301-541 | A |
| O00482 | 5L0M | A=79-187 | A |
| O00482 | 5SYZ | A=297-538 | A |
| O00482 | 4IS8 | A/B=300-538 | A |
| O00482 | 2A66 | A=79-187 | A |
| O00482 | 1YOK | A=300-541 | A |
| O00482 | 4RWV | A=294-541 | A |
| O14646 | 5AFW | A=270-443 | A |
| O14646 | 2B2Y | A/B=268-443,C=268-373 | A |
| O14646 | 2B2U | C=268-373,A/B=268-443 | C |
| O14646 | 2N39 | A=1409-1511 | A |
| O14646 | 4O42 | A=268-443 | A |
| O14646 | 4B4C | A=1119-1327 | A |
| O14646 | 2B2V | C=268-373,A/B=268-443 | C |
| O14646 | 2B2T | C=268-373,A/B=268-443 | C |
| O14646 | 4NW2 | A/C=268-443 | A |
| O14646 | 2B2W | C=268-373,A/B=268-443 | C |
| O00571 | 2JGN | A/B/C=409-580 | A |
| O00571 | 4PXA | A=135-582 | A |
| O00571 | 5E7J | A=133-584 | A |
| O00571 | 4O2E | C/F=2-10 | C |
| O00571 | 3JRV | C/D/E=71-90 | C |
| O00571 | 2I4I | A=168-582 | A |
| O00571 | 5E7M | A=133-584 | A |
| O00571 | 4O2C | C=2-10 | C |
| O00571 | 6CZ5 | A=132-607 | A |
| O00571 | 4PX9 | A/B/C=135-407 | A |
| O00571 | 5E7I | A/B/C=133-584 | A |
| O00571 | 4O2F | C/F=3-10 | C |
| O00257 | 5EPL | A/B=8-65 | A |
| O00257 | 3I8Z | A=8-62 | A |
| O00257 | 2K28 | A=8-65 | A |
| O00287 | 2KW3 | C=214-272 | C |
| O00255 | 4OG7 | A=74-386,A=549-593,A=1-53,A=399-459 | A |
| O00255 | 3U85 | A=2-459,A=520-610 | A |
| O00255 | 3U84 | A/B=520-610,A/B=2-459 | A |
| O00255 | 4GQ6 | A=537-593,A=1-53,A=399-459,A=74-386 | A |
| O00255 | 4GQ3 | A=74-386,A=537-593,A=399-459,A=1-53 | A |
| O00255 | 6BXH | A=1-386,A=399-459,A=537-593 | A |
| O00255 | 4X5Y | A=74-386,A=399-459,A=1-53,A=537-593 | A |
| O00255 | 5DDE | A=1-53,A=399-459,A=537-593,A=74-386 | A |
| O00255 | 3U86 | A=2-459,A=520-610 | A |
| O00255 | 5DDA | A=399-459,A=537-593,A=1-53,A=74-386 | A |
| O00255 | 4OG4 | A=399-459,A=549-593,A=74-386,A=1-53 | A |
| O00255 | 5DB1 | A=74-386,A=537-593,A=399-459,A=1-53 | A |
| O00255 | 4GPQ | A=1-53,A=74-386,A=537-593,A=399-459 | A |
| O00255 | 5DB2 | A=1-53,A=399-459,A=537-593,A=74-386 | A |
| O00255 | 5DDC | A=537-593,A=74-386,A=1-53,A=399-459 | A |
| O00255 | 6B41 | A=2-459,A=520-610 | A |
| O00255 | 4X5Z | A=1-53,A=399-459,A=537-593,A=74-386 | A |
| O00255 | 6E1A | A=2-459,A=520-610 | A |
| O00255 | 5DD9 | A=74-386,A=399-459,A=537-593,A=1-53 | A |
| O00255 | 4I80 | A=520-610,A=2-458 | A |
| O00255 | 4OG5 | A=1-53,A=399-459,A=549-593,A=74-386 | A |
| O00255 | 4OG8 | A=549-593,A=399-459,A=1-53,A=74-386 | A |
| O00255 | 6BXY | A=1-53,A=399-459,A=74-386,A=537-593 | A |
| O00255 | 5DDF | A=537-593,A=74-386,A=399-459,A=1-53 | A |
| O00255 | 5DB3 | A=74-386,A=399-459,A=537-593,A=1-53 | A |
| O00255 | 6BY8 | A=399-459,A=74-386,A=1-53,A=537-593 | A |
| O00255 | 5DB0 | A=1-53,A=399-459,A=537-593,A=74-386 | A |
| O00255 | 4OG6 | A=74-386,A=549-593,A=1-53,A=399-459 | A |
| O00255 | 5DDD | A=1-53,A=399-459,A=537-593,A=74-386 | A |
| O00255 | 5DDB | A=74-386,A=1-53,A=537-593,A=399-459 | A |
| O00255 | 4GQ4 | A=1-53,A=537-593,A=399-459,A=74-386 | A |
| O00255 | 4OG3 | A=1-53,A=399-459,A=549-593,A=74-386 | A |
| O00255 | 3U88 | A/B=520-610,A/B=2-459 | A |
| O14593 | 3V30 | A=90-260 | A |
| O14593 | 3UXG | A=90-260 | A |
| O14593 | 6MEW | A/C=90-260 | A |
| A8MT69 | 4DRB | J/K/L/M/N/O=1-81 | J |
| A8MT69 | 4NE3 | B=8-81 | B |
| A8MT69 | 4E45 | B/D/G/I/L/N=1-81 | B |
| A8MT69 | 4NE6 | B/D=8-81 | B |
| A8MT69 | 4NDY | B/D/H/L/M/N/U/V/W/X=8-81 | B |
| A8MT69 | 4NE5 | B/D/F/H=8-81 | B |
| A8MT69 | 4DRA | E/F/G/H=1-81 | E |
| A8MT69 | 4E44 | B/D=1-81 | B |
| A8MT69 | 4NE1 | B/D/H/L/M/N/U/V/W/X/Z/b/d/h/i/j/o/p/q/r=8-81 | B |
| O00327 | 4H10 | A=66-128 | A |
| O00470 | 4XRS | A/B=279-336 | A |
| O00470 | 5EGO | A=279-333 | A |
| A9YTQ3 | 5Y7Y | A=27-280 | A |
In [7]:
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%sql SELECT * FROM alphafolds LIMIT 1
%sql SELECT * FROM alphafolds LIMIT 1
Running query in 'DuckDBPyConnection'
Out[7]:
| uniprot_acc | summary | bcif_file | cif_file | pdb_file | pae_doc_file | am_annotations_file | am_annotations_hg19_file | am_annotations_hg38_file | msa_file | plddt_doc_file |
|---|---|---|---|---|---|---|---|---|---|---|
| A0A087WUV0 | {"allVersions":[1,2,3,4,5,6],"bcifUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-model_v6.bcif","cifUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-model_v6.cif","entityType":"protein","fractionPlddtConfident":0.251,"fractionPlddtLow":0.088,"fractionPlddtVeryHigh":0.289,"fractionPlddtVeryLow":0.372,"globalMetricValue":66.62,"isUniProt":true,"latestVersion":6,"modelCreatedDate":"2025-08-01T00:00:00Z","modelEntityId":"AF-A0A087WUV0-F1","paeDocUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-predicted_aligned_error_v6.json","pdbUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-model_v6.pdb","providerId":"GDM","sequence":"MEPEGRGSLFEDSDLLHAGNPKENDVTAVLLTPGSQELMIRDMAEALTQWRQLNSPQGDVPEKPRNLVLLGLPISTPDVISQLEHEEELEREVSKAASQKHWETIPESKELTPEKDISEEESAPGVLIVRFSKESSSECEDSLESQQENHEKHLIQEAVTEKSSRERSYQSDEFRRNCTQRSLLVQQQGERLHHCDSFKNNLKQNSDIIRHERICAGKKPWKCNECEKAFSYYSAFVLHQRIHTGEKPYECNECGKAFSQSIHLTLHQRIHTGEKPYECHECGKAFSHRSALIRHHIIHTGEKPYECNECGKAFNQSSYLTQHQRIHTGEKPYECNECGKAFSQSTFLTQHQVIHTGEKPYKCNECGKAFSDRSGLIQHQRTHTGERPYECNECGKAFGYCSALTQHQRTHTGEKPYKCNDCAKAFSDRSALIRHQRTHTGEKPYKCKDCGKAFSQSSSLTKHQKTHTGEKPYKCKECGKAFSQSSSLSQHQKTHAGVKTKKYVQALSEHLTFGQHKRIHTG","sequenceChecksum":"5DE83E4BE25B68BD","sequenceEnd":522,"sequenceStart":1,"sequenceVersionDate":"2014-10-29T00:00:00Z","toolUsed":"AlphaFold Monomer v2.0 pipeline","alternativeNames":null,"amAnnotationsHg19Url":null,"amAnnotationsHg38Url":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-hg38.csv","amAnnotationsUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-aa-substitutions.csv","catalyticActivities":null,"complexName":null,"functions":null,"gene":"ZNF892","geneSynonyms":null,"ipSAE":null,"ipTM":null,"isUniProtReferenceProteome":true,"isUniProtReviewed":true,"keywords":null,"msaUrl":"https://alphafold.ebi.ac.uk/files/msa/AF-A0A087WUV0-F1-msa_v6.a3m","organismCommonNames":null,"organismScientificName":"Homo sapiens","organismSynonyms":null,"plddtDocUrl":"https://alphafold.ebi.ac.uk/files/AF-A0A087WUV0-F1-confidence_v6.json","proteinFullNames":null,"proteinShortNames":null,"stoichiometry":null,"taxId":9606,"taxonomyLineage":null,"uniprotAccession":"A0A087WUV0","uniprotDescription":"Zinc finger protein 892","uniprotId":"ZN892_HUMAN"} | None | downloads/alphafold/AF-A0A087WUV0-F1-model_v6.cif.gz | None | None | None | None | None | None | None |
In [8]:
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%sql SELECT count(*) FROM alphafolds
%sql SELECT count(*) FROM alphafolds
Running query in 'DuckDBPyConnection'
Out[8]:
| count_star() |
|---|
| 100 |
In [9]:
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# Fetch fields from inside summary
%sql SELECT uniprot_acc, summary.taxId, summary.gene, summary.organismScientificName FROM alphafolds
# Fetch fields from inside summary
%sql SELECT uniprot_acc, summary.taxId, summary.gene, summary.organismScientificName FROM alphafolds
Running query in 'DuckDBPyConnection'
Out[9]:
| uniprot_acc | taxId | gene | organismScientificName |
|---|---|---|---|
| A0A087WUV0 | 9606 | "ZNF892" | "Homo sapiens" |
| A0A0C5B5G6 | 9606 | "MT-RNR1" | "Homo sapiens" |
| A0A0U1RQI7 | 9606 | "KLF18" | "Homo sapiens" |
| A0A1B0GTS1 | 9606 | "HSFX4" | "Homo sapiens" |
| A0A1B0GVZ6 | 9606 | "MBD3L2B" | "Homo sapiens" |
| A0A1B0GWH4 | 9606 | "HSFX3" | "Homo sapiens" |
| A0A1W2PPF3 | 9606 | "DUXB" | "Homo sapiens" |
| A0A1W2PPK0 | 9606 | "CPHXL2" | "Homo sapiens" |
| A0A1W2PPM1 | 9606 | "CPHXL" | "Homo sapiens" |
| A0A1W2PQ73 | 9606 | "ERFL" | "Homo sapiens" |
| A0A1W2PQL4 | 9606 | "ZNF722" | "Homo sapiens" |
| A0A1W2PRP0 | 9606 | "FOXL3" | "Homo sapiens" |
| A0A2R8Y619 | 9606 | "H2BK1" | "Homo sapiens" |
| A0A2Z4LIS9 | 9606 | "FOXO3B" | "Homo sapiens" |
| A0A3B3IU63 | 9606 | "H2AL3" | "Homo sapiens" |
| A0A5F9ZHS7 | 9606 | "NFILZ" | "Homo sapiens" |
| A1A519 | 9606 | "FAM170A" | "Homo sapiens" |
| A1YPR0 | 9606 | "ZBTB7C" | "Homo sapiens" |
| A2RRD8 | 9606 | "ZNF320" | "Homo sapiens" |
| A2RU54 | 9606 | "HMX2" | "Homo sapiens" |
| A3KN83 | 9606 | "SBNO1" | "Homo sapiens" |
| A6NCS4 | 9606 | "NKX2-6" | "Homo sapiens" |
| A6NDR6 | 9606 | "MEIS3P1" | "Homo sapiens" |
| A6NDX5 | 9606 | "ZNF840P" | "Homo sapiens" |
| A6NDZ8 | 9606 | "MBD3L4" | "Homo sapiens" |
| A6NE82 | 9606 | "MBD3L3" | "Homo sapiens" |
| A6NFD8 | 9606 | "HELT" | "Homo sapiens" |
| A6NFI3 | 9606 | "ZNF316" | "Homo sapiens" |
| A6NFQ7 | 9606 | "DPRX" | "Homo sapiens" |
| A6NGD5 | 9606 | "ZSCAN5C" | "Homo sapiens" |
| A6NHJ4 | 9606 | "ZNF860" | "Homo sapiens" |
| A6NHT5 | 9606 | "HMX3" | "Homo sapiens" |
| A6NI15 | 9606 | "MSGN1" | "Homo sapiens" |
| A6NJ08 | 9606 | "MBD3L5" | "Homo sapiens" |
| A6NJ46 | 9606 | "NKX6-3" | "Homo sapiens" |
| A6NJG6 | 9606 | "ARGFX" | "Homo sapiens" |
| A6NJL1 | 9606 | "ZSCAN5B" | "Homo sapiens" |
| A6NJT0 | 9606 | "UNCX" | "Homo sapiens" |
| A6NK53 | 9606 | "ZNF233" | "Homo sapiens" |
| A6NK75 | 9606 | "ZNF98" | "Homo sapiens" |
| A6NKF2 | 9606 | "ARID3C" | "Homo sapiens" |
| A6NLW8 | 9606 | "DUXA" | "Homo sapiens" |
| A6NM28 | 9606 | "ZFP92" | "Homo sapiens" |
| A6NMT0 | 9606 | "DBX1" | "Homo sapiens" |
| A6NN14 | 9606 | "ZNF729" | "Homo sapiens" |
| A6NNA5 | 9606 | "DRGX" | "Homo sapiens" |
| A6NNF4 | 9606 | "ZNF726" | "Homo sapiens" |
| A6NP11 | 9606 | "ZNF716" | "Homo sapiens" |
| A8K0S8 | 9606 | "MEIS3P2" | "Homo sapiens" |
| A8K830 | 9606 | "POU2AF3" | "Homo sapiens" |
| A8K8V0 | 9606 | "ZNF785" | "Homo sapiens" |
| A8MPP1 | 9606 | "DDX11L8" | "Homo sapiens" |
| A8MQ14 | 9606 | "ZNF850" | "Homo sapiens" |
| A8MT65 | 9606 | "ZNF891" | "Homo sapiens" |
| A8MT69 | 9606 | "CENPX" | "Homo sapiens" |
| A8MTJ6 | 9606 | "FOXI3" | "Homo sapiens" |
| A8MTQ0 | 9606 | "NOTO" | "Homo sapiens" |
| A8MTY0 | 9606 | "ZNF724" | "Homo sapiens" |
| A8MUV8 | 9606 | "ZNF727" | "Homo sapiens" |
| A8MUZ8 | 9606 | "ZNF705G" | "Homo sapiens" |
| A8MWA4 | 9606 | "ZNF705EP" | "Homo sapiens" |
| A8MXY4 | 9606 | "ZNF99" | "Homo sapiens" |
| A8MYZ6 | 9606 | "FOXO6" | "Homo sapiens" |
| A8MZ59 | 9606 | "LEUTX" | "Homo sapiens" |
| A9YTQ3 | 9606 | "AHRR" | "Homo sapiens" |
| B1APH4 | 9606 | "ZNF487" | "Homo sapiens" |
| B2RD01 | 9606 | "CENPBD1P" | "Homo sapiens" |
| B2RPK0 | 9606 | "HMGB1P1" | "Homo sapiens" |
| B2RXF5 | 9606 | "ZBTB42" | "Homo sapiens" |
| B4DU55 | 9606 | "ZNF879" | "Homo sapiens" |
| B4DX44 | 9606 | "ZNF736" | "Homo sapiens" |
| B4DXR9 | 9606 | "ZNF732" | "Homo sapiens" |
| C9JN71 | 9606 | "ZNF878" | "Homo sapiens" |
| C9JSJ3 | 9606 | "MEIOSIN" | "Homo sapiens" |
| E7ETH6 | 9606 | "ZNF587B" | "Homo sapiens" |
| E9PAV3 | 9606 | "NACA" | "Homo sapiens" |
| E9PGG2 | 9606 | "ANHX" | "Homo sapiens" |
| O00110 | 9606 | "OVOL3" | "Homo sapiens" |
| O00255 | 9606 | "MEN1" | "Homo sapiens" |
| O00257 | 9606 | "CBX4" | "Homo sapiens" |
| O00268 | 9606 | "TAF4" | "Homo sapiens" |
| O00287 | 9606 | "RFXAP" | "Homo sapiens" |
| O00321 | 9606 | "ETV2" | "Homo sapiens" |
| O00327 | 9606 | "BMAL1" | "Homo sapiens" |
| O00358 | 9606 | "FOXE1" | "Homo sapiens" |
| O00409 | 9606 | "FOXN3" | "Homo sapiens" |
| O00470 | 9606 | "MEIS1" | "Homo sapiens" |
| O00479 | 9606 | "HMGN4" | "Homo sapiens" |
| O00482 | 9606 | "NR5A2" | "Homo sapiens" |
| O00570 | 9606 | "SOX1" | "Homo sapiens" |
| O00571 | 9606 | "DDX3X" | "Homo sapiens" |
| O00712 | 9606 | "NFIB" | "Homo sapiens" |
| O00716 | 9606 | "E2F3" | "Homo sapiens" |
| O14497 | 9606 | "ARID1A" | "Homo sapiens" |
| O14503 | 9606 | "BHLHE40" | "Homo sapiens" |
| O14529 | 9606 | "CUX2" | "Homo sapiens" |
| O14593 | 9606 | "RFXANK" | "Homo sapiens" |
| O14627 | 9606 | "CDX4" | "Homo sapiens" |
| O14628 | 9606 | "ZNF195" | "Homo sapiens" |
| O14646 | 9606 | "CHD1" | "Homo sapiens" |
Sequence length of Uniprot protein and alphafold entry
In [11]:
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%%sql
SELECT uniprot_acc,
proteins.sequence_length,
summary.sequenceStart, summary.sequenceEnd
FROM proteins
JOIN alphafolds USING (uniprot_acc)
LIMIT 10
%%sql
SELECT uniprot_acc,
proteins.sequence_length,
summary.sequenceStart, summary.sequenceEnd
FROM proteins
JOIN alphafolds USING (uniprot_acc)
LIMIT 10
Running query in 'DuckDBPyConnection'
Out[11]:
| uniprot_acc | sequence_length | sequenceStart | sequenceEnd |
|---|---|---|---|
| A0A087WUV0 | 522 | 1 | 522 |
| A0A0C5B5G6 | 16 | 1 | 16 |
| A0A0U1RQI7 | 1052 | 1 | 1052 |
| A0A1B0GTS1 | 333 | 1 | 333 |
| A0A1B0GVZ6 | 204 | 1 | 204 |
| A0A1B0GWH4 | 333 | 1 | 333 |
| A0A1W2PPF3 | 345 | 1 | 345 |
| A0A1W2PPK0 | 400 | 1 | 400 |
| A0A1W2PPM1 | 405 | 1 | 405 |
| A0A1W2PQ73 | 354 | 1 | 354 |
Density filtered models¶
In [10]:
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%%sql
SELECT
f.confidence, f.min_threshold, f.max_threshold,
density_filtered_alphafolds.*,
alphafolds.summary.uniprotStart,
alphafolds.summary.uniprotEnd,
length(alphafolds.summary.uniprotSequence) AS uniprot_length
FROM density_filtered_alphafolds
JOIN density_filters AS f USING (density_filter_id)
JOIN alphafolds USING (uniprot_acc)
LIMIT 100;
%%sql
SELECT
f.confidence, f.min_threshold, f.max_threshold,
density_filtered_alphafolds.*,
alphafolds.summary.uniprotStart,
alphafolds.summary.uniprotEnd,
length(alphafolds.summary.uniprotSequence) AS uniprot_length
FROM density_filtered_alphafolds
JOIN density_filters AS f USING (density_filter_id)
JOIN alphafolds USING (uniprot_acc)
LIMIT 100;
Running query in 'DuckDBPyConnection'
Out[10]:
| confidence | min_threshold | max_threshold | density_filter_id | uniprot_acc | nr_residues_above_confidence | keep | pdb_file | uniprotStart | uniprotEnd | uniprot_length |
|---|---|---|---|---|---|---|---|---|---|---|
| 70.0 | 100 | 500 | 1 | A0A087WUV0 | 283 | True | density_filtered/AF-A0A087WUV0-F1-model_v4.pdb | 1 | 522 | 524 |
| 70.0 | 100 | 500 | 1 | A0A0C5B5G6 | 10 | False | None | 1 | 16 | 18 |
| 70.0 | 100 | 500 | 1 | A0A0U1RQI7 | 192 | True | density_filtered/AF-A0A0U1RQI7-F1-model_v4.pdb | 1 | 1052 | 1054 |
| 70.0 | 100 | 500 | 1 | A0A1B0GTS1 | 116 | True | density_filtered/AF-A0A1B0GTS1-F1-model_v4.pdb | 1 | 333 | 335 |
| 70.0 | 100 | 500 | 1 | A0A1B0GVZ6 | 54 | False | None | 1 | 204 | 206 |
| 70.0 | 100 | 500 | 1 | A0A1B0GWH4 | 117 | True | density_filtered/AF-A0A1B0GWH4-F1-model_v4.pdb | 1 | 333 | 335 |
| 70.0 | 100 | 500 | 1 | A0A1W2PPF3 | 124 | True | density_filtered/AF-A0A1W2PPF3-F1-model_v4.pdb | 1 | 345 | 347 |
| 70.0 | 100 | 500 | 1 | A0A1W2PPK0 | 71 | False | None | 1 | 400 | 402 |
| 70.0 | 100 | 500 | 1 | A0A1W2PPM1 | 68 | False | None | 1 | 405 | 407 |
| 70.0 | 100 | 500 | 1 | A0A1W2PQ73 | 86 | False | None | 1 | 354 | 356 |
| 70.0 | 100 | 500 | 1 | A0A1W2PQL4 | 226 | True | density_filtered/AF-A0A1W2PQL4-F1-model_v4.pdb | 1 | 384 | 386 |
| 70.0 | 100 | 500 | 1 | A0A1W2PRP0 | 94 | False | None | 1 | 233 | 235 |
| 70.0 | 100 | 500 | 1 | A0A2R8Y619 | 92 | False | None | 1 | 122 | 124 |
| 70.0 | 100 | 500 | 1 | A0A2Z4LIS9 | 52 | False | None | 1 | 290 | 292 |
| 70.0 | 100 | 500 | 1 | A0A3B3IU63 | 92 | False | None | 1 | 148 | 150 |
| 70.0 | 100 | 500 | 1 | A0A5F9ZHS7 | 71 | False | None | 1 | 289 | 291 |
| 70.0 | 100 | 500 | 1 | A1A519 | 64 | False | None | 1 | 330 | 332 |
| 70.0 | 100 | 500 | 1 | A1YPR0 | 214 | True | density_filtered/AF-A1YPR0-F1-model_v4.pdb | 1 | 619 | 621 |
| 70.0 | 100 | 500 | 1 | A2RRD8 | 336 | True | density_filtered/AF-A2RRD8-F1-model_v4.pdb | 1 | 509 | 511 |
| 70.0 | 100 | 500 | 1 | A2RU54 | 83 | False | None | 1 | 273 | 275 |
| 70.0 | 100 | 500 | 1 | A3KN83 | 844 | False | None | 1 | 1393 | 1395 |
| 70.0 | 100 | 500 | 1 | A6NCS4 | 75 | False | None | 1 | 301 | 303 |
| 70.0 | 100 | 500 | 1 | A6NDR6 | 94 | False | None | 1 | 274 | 276 |
| 70.0 | 100 | 500 | 1 | A6NDX5 | 418 | True | density_filtered/AF-A6NDX5-F1-model_v4.pdb | 1 | 716 | 718 |
| 70.0 | 100 | 500 | 1 | A6NDZ8 | 64 | False | None | 1 | 208 | 210 |
| 70.0 | 100 | 500 | 1 | A6NE82 | 60 | False | None | 1 | 208 | 210 |
| 70.0 | 100 | 500 | 1 | A6NFD8 | 100 | True | density_filtered/AF-A6NFD8-F1-model_v4.pdb | 1 | 242 | 244 |
| 70.0 | 100 | 500 | 1 | A6NFI3 | 458 | True | density_filtered/AF-A6NFI3-F1-model_v4.pdb | 1 | 1004 | 1006 |
| 70.0 | 100 | 500 | 1 | A6NFQ7 | 76 | False | None | 1 | 191 | 193 |
| 70.0 | 100 | 500 | 1 | A6NGD5 | 206 | True | density_filtered/AF-A6NGD5-F1-model_v4.pdb | 1 | 496 | 498 |
| 70.0 | 100 | 500 | 1 | A6NHJ4 | 378 | True | density_filtered/AF-A6NHJ4-F1-model_v4.pdb | 1 | 632 | 634 |
| 70.0 | 100 | 500 | 1 | A6NHT5 | 97 | False | None | 1 | 357 | 359 |
| 70.0 | 100 | 500 | 1 | A6NJ08 | 61 | False | None | 1 | 208 | 210 |
| 70.0 | 100 | 500 | 1 | A6NJ46 | 81 | False | None | 1 | 265 | 267 |
| 70.0 | 100 | 500 | 1 | A6NJG6 | 66 | False | None | 1 | 315 | 317 |
| 70.0 | 100 | 500 | 1 | A6NJL1 | 220 | True | density_filtered/AF-A6NJL1-F1-model_v4.pdb | 1 | 495 | 497 |
| 70.0 | 100 | 500 | 1 | A6NJT0 | 102 | True | density_filtered/AF-A6NJT0-F1-model_v4.pdb | 1 | 531 | 533 |
| 70.0 | 100 | 500 | 1 | A6NK53 | 218 | True | density_filtered/AF-A6NK53-F1-model_v4.pdb | 1 | 670 | 672 |
| 70.0 | 100 | 500 | 1 | A6NK75 | 412 | True | density_filtered/AF-A6NK75-F1-model_v4.pdb | 1 | 572 | 574 |
| 70.0 | 100 | 500 | 1 | A6NKF2 | 150 | True | density_filtered/AF-A6NKF2-F1-model_v4.pdb | 1 | 412 | 414 |
| 70.0 | 100 | 500 | 1 | A6NLW8 | 120 | True | density_filtered/AF-A6NLW8-F1-model_v4.pdb | 1 | 204 | 206 |
| 70.0 | 100 | 500 | 1 | A6NM28 | 276 | True | density_filtered/AF-A6NM28-F1-model_v4.pdb | 1 | 416 | 418 |
| 70.0 | 100 | 500 | 1 | A6NMT0 | 77 | False | None | 1 | 343 | 345 |
| 70.0 | 100 | 500 | 1 | A6NN14 | 795 | False | None | 1 | 1252 | 1254 |
| 70.0 | 100 | 500 | 1 | A6NNF4 | 525 | False | None | 1 | 738 | 740 |
| 70.0 | 100 | 500 | 1 | A6NP11 | 314 | True | density_filtered/AF-A6NP11-F1-model_v4.pdb | 1 | 495 | 497 |
| 70.0 | 100 | 500 | 1 | A8K0S8 | 111 | True | density_filtered/AF-A8K0S8-F1-model_v4.pdb | 1 | 358 | 360 |
| 70.0 | 100 | 500 | 1 | A8K830 | 10 | False | None | 1 | 154 | 156 |
| 70.0 | 100 | 500 | 1 | A8K8V0 | 214 | True | density_filtered/AF-A8K8V0-F1-model_v4.pdb | 1 | 405 | 407 |
| 70.0 | 100 | 500 | 1 | A8MPP1 | 706 | False | None | 1 | 907 | 909 |
| 70.0 | 100 | 500 | 1 | A8MQ14 | 811 | False | None | 1 | 1090 | 1092 |
| 70.0 | 100 | 500 | 1 | A8MT65 | 246 | True | density_filtered/AF-A8MT65-F1-model_v4.pdb | 1 | 544 | 546 |
| 70.0 | 100 | 500 | 1 | A8MT69 | 74 | False | None | 1 | 81 | 83 |
| 70.0 | 100 | 500 | 1 | A8MTJ6 | 94 | False | None | 1 | 420 | 422 |
| 70.0 | 100 | 500 | 1 | A8MTQ0 | 89 | False | None | 1 | 251 | 253 |
| 70.0 | 100 | 500 | 1 | A8MTY0 | 483 | True | density_filtered/AF-A8MTY0-F1-model_v4.pdb | 1 | 619 | 621 |
| 70.0 | 100 | 500 | 1 | A8MUV8 | 326 | True | density_filtered/AF-A8MUV8-F1-model_v4.pdb | 1 | 499 | 501 |
| 70.0 | 100 | 500 | 1 | A8MUZ8 | 137 | True | density_filtered/AF-A8MUZ8-F1-model_v4.pdb | 1 | 300 | 302 |
| 70.0 | 100 | 500 | 1 | A8MWA4 | 101 | True | density_filtered/AF-A8MWA4-F1-model_v4.pdb | 1 | 300 | 302 |
| 70.0 | 100 | 500 | 1 | A8MXY4 | 657 | False | None | 1 | 864 | 866 |
| 70.0 | 100 | 500 | 1 | A8MYZ6 | 90 | False | None | 1 | 492 | 494 |
| 70.0 | 100 | 500 | 1 | A8MZ59 | 78 | False | None | 1 | 198 | 200 |
| 70.0 | 100 | 500 | 1 | A9YTQ3 | 196 | True | density_filtered/AF-A9YTQ3-F1-model_v4.pdb | 1 | 701 | 703 |
| 70.0 | 100 | 500 | 1 | B1APH4 | 67 | False | None | 1 | 448 | 450 |
| 70.0 | 100 | 500 | 1 | B2RD01 | 54 | False | None | 1 | 187 | 189 |
| 70.0 | 100 | 500 | 1 | B2RPK0 | 151 | True | density_filtered/AF-B2RPK0-F1-model_v4.pdb | 1 | 211 | 213 |
| 70.0 | 100 | 500 | 1 | B2RXF5 | 94 | False | None | 1 | 422 | 424 |
| 70.0 | 100 | 500 | 1 | B4DU55 | 375 | True | density_filtered/AF-B4DU55-F1-model_v4.pdb | 1 | 563 | 565 |
| 70.0 | 100 | 500 | 1 | B4DX44 | 290 | True | density_filtered/AF-B4DX44-F1-model_v4.pdb | 1 | 427 | 429 |
| 70.0 | 100 | 500 | 1 | A6NI15 | 66 | False | None | 1 | 193 | 195 |
| 70.0 | 100 | 500 | 1 | A6NNA5 | 85 | False | None | 1 | 263 | 265 |
Powerfit¶
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result = %sql SELECT powerfit_run_id, options.target, options.resolution FROM powerfit_runs;
result = %sql SELECT powerfit_run_id, options.target, options.resolution FROM powerfit_runs;
Running query in 'DuckDBPyConnection'
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result
result
Out[12]:
| powerfit_run_id | target | resolution |
|---|---|---|
| 1 | "../../powerfit-tutorial/ribosome-KsgA.map" | 13 |
In [13]:
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%%sql
SELECT density_filter_id, uniprot_acc, pdb_file,
parse_filename(pdb_file, true) AS pdb_filename
FROM density_filtered_alphafolds WHERE keep=True
%%sql
SELECT density_filter_id, uniprot_acc, pdb_file,
parse_filename(pdb_file, true) AS pdb_filename
FROM density_filtered_alphafolds WHERE keep=True
Running query in 'DuckDBPyConnection'
Out[13]:
| density_filter_id | uniprot_acc | pdb_file | pdb_filename |
|---|---|---|---|
| 1 | A0A087WUV0 | density_filtered/AF-A0A087WUV0-F1-model_v4.pdb | AF-A0A087WUV0-F1-model_v4 |
| 1 | A0A0U1RQI7 | density_filtered/AF-A0A0U1RQI7-F1-model_v4.pdb | AF-A0A0U1RQI7-F1-model_v4 |
| 1 | A0A1B0GTS1 | density_filtered/AF-A0A1B0GTS1-F1-model_v4.pdb | AF-A0A1B0GTS1-F1-model_v4 |
| 1 | A0A1B0GWH4 | density_filtered/AF-A0A1B0GWH4-F1-model_v4.pdb | AF-A0A1B0GWH4-F1-model_v4 |
| 1 | A0A1W2PPF3 | density_filtered/AF-A0A1W2PPF3-F1-model_v4.pdb | AF-A0A1W2PPF3-F1-model_v4 |
| 1 | A0A1W2PQL4 | density_filtered/AF-A0A1W2PQL4-F1-model_v4.pdb | AF-A0A1W2PQL4-F1-model_v4 |
| 1 | A1YPR0 | density_filtered/AF-A1YPR0-F1-model_v4.pdb | AF-A1YPR0-F1-model_v4 |
| 1 | A2RRD8 | density_filtered/AF-A2RRD8-F1-model_v4.pdb | AF-A2RRD8-F1-model_v4 |
| 1 | A6NDX5 | density_filtered/AF-A6NDX5-F1-model_v4.pdb | AF-A6NDX5-F1-model_v4 |
| 1 | A6NFD8 | density_filtered/AF-A6NFD8-F1-model_v4.pdb | AF-A6NFD8-F1-model_v4 |
| 1 | A6NFI3 | density_filtered/AF-A6NFI3-F1-model_v4.pdb | AF-A6NFI3-F1-model_v4 |
| 1 | A6NGD5 | density_filtered/AF-A6NGD5-F1-model_v4.pdb | AF-A6NGD5-F1-model_v4 |
| 1 | A6NHJ4 | density_filtered/AF-A6NHJ4-F1-model_v4.pdb | AF-A6NHJ4-F1-model_v4 |
| 1 | A6NJL1 | density_filtered/AF-A6NJL1-F1-model_v4.pdb | AF-A6NJL1-F1-model_v4 |
| 1 | A6NJT0 | density_filtered/AF-A6NJT0-F1-model_v4.pdb | AF-A6NJT0-F1-model_v4 |
| 1 | A6NK53 | density_filtered/AF-A6NK53-F1-model_v4.pdb | AF-A6NK53-F1-model_v4 |
| 1 | A6NK75 | density_filtered/AF-A6NK75-F1-model_v4.pdb | AF-A6NK75-F1-model_v4 |
| 1 | A6NKF2 | density_filtered/AF-A6NKF2-F1-model_v4.pdb | AF-A6NKF2-F1-model_v4 |
| 1 | A6NLW8 | density_filtered/AF-A6NLW8-F1-model_v4.pdb | AF-A6NLW8-F1-model_v4 |
| 1 | A6NM28 | density_filtered/AF-A6NM28-F1-model_v4.pdb | AF-A6NM28-F1-model_v4 |
| 1 | A6NP11 | density_filtered/AF-A6NP11-F1-model_v4.pdb | AF-A6NP11-F1-model_v4 |
| 1 | A8K0S8 | density_filtered/AF-A8K0S8-F1-model_v4.pdb | AF-A8K0S8-F1-model_v4 |
| 1 | A8K8V0 | density_filtered/AF-A8K8V0-F1-model_v4.pdb | AF-A8K8V0-F1-model_v4 |
| 1 | A8MT65 | density_filtered/AF-A8MT65-F1-model_v4.pdb | AF-A8MT65-F1-model_v4 |
| 1 | A8MTY0 | density_filtered/AF-A8MTY0-F1-model_v4.pdb | AF-A8MTY0-F1-model_v4 |
| 1 | A8MUV8 | density_filtered/AF-A8MUV8-F1-model_v4.pdb | AF-A8MUV8-F1-model_v4 |
| 1 | A8MUZ8 | density_filtered/AF-A8MUZ8-F1-model_v4.pdb | AF-A8MUZ8-F1-model_v4 |
| 1 | A8MWA4 | density_filtered/AF-A8MWA4-F1-model_v4.pdb | AF-A8MWA4-F1-model_v4 |
| 1 | A9YTQ3 | density_filtered/AF-A9YTQ3-F1-model_v4.pdb | AF-A9YTQ3-F1-model_v4 |
| 1 | B2RPK0 | density_filtered/AF-B2RPK0-F1-model_v4.pdb | AF-B2RPK0-F1-model_v4 |
| 1 | B4DU55 | density_filtered/AF-B4DU55-F1-model_v4.pdb | AF-B4DU55-F1-model_v4 |
| 1 | B4DX44 | density_filtered/AF-B4DX44-F1-model_v4.pdb | AF-B4DX44-F1-model_v4 |
In [14]:
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%%sql
SELECT uniprot_acc, pdb_id, single_chain_pdb_file,
parse_filename(single_chain_pdb_file, true) AS structure
FROM proteins_pdbs
WHERE single_chain_pdb_file IS NOT NULL
%%sql
SELECT uniprot_acc, pdb_id, single_chain_pdb_file,
parse_filename(single_chain_pdb_file, true) AS structure
FROM proteins_pdbs
WHERE single_chain_pdb_file IS NOT NULL
Running query in 'DuckDBPyConnection'
Out[14]:
| uniprot_acc | pdb_id | single_chain_pdb_file | structure |
|---|---|---|---|
| A8MT69 | 7YWX | single_chain/A8MT69_7ywx_X2A.pdb | A8MT69_7ywx_X2A |
| A8MT69 | 4NE5 | single_chain/A8MT69_4ne5_B2A.pdb | A8MT69_4ne5_B2A |
| A8MT69 | 4E45 | single_chain/A8MT69_4e45_B2A.pdb | A8MT69_4e45_B2A |
| A8MT69 | 4NDY | single_chain/A8MT69_4ndy_B2A.pdb | A8MT69_4ndy_B2A |
| A8MT69 | 4NE3 | single_chain/A8MT69_4ne3_B2A.pdb | A8MT69_4ne3_B2A |
| A8MT69 | 4E44 | single_chain/A8MT69_4e44_B2A.pdb | A8MT69_4e44_B2A |
| A8MT69 | 4NE6 | single_chain/A8MT69_4ne6_B2A.pdb | A8MT69_4ne6_B2A |
| A8MT69 | 7R5S | single_chain/A8MT69_7r5s_X2A.pdb | A8MT69_7r5s_X2A |
| A8MT69 | 7XHN | single_chain/A8MT69_7xhn_X2A.pdb | A8MT69_7xhn_X2A |
| A8MT69 | 7XHO | single_chain/A8MT69_7xho_X2A.pdb | A8MT69_7xho_X2A |
| A8MT69 | 4DRA | single_chain/A8MT69_4dra_E2A.pdb | A8MT69_4dra_E2A |
| A8MT69 | 4NE1 | single_chain/A8MT69_4ne1_B2A.pdb | A8MT69_4ne1_B2A |
| A8MT69 | 4DRB | single_chain/A8MT69_4drb_J2A.pdb | A8MT69_4drb_J2A |
| A9YTQ3 | 5Y7Y | single_chain/A9YTQ3_5y7y_A2A.pdb | A9YTQ3_5y7y_A2A |
In [15]:
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from protein_detective.db import powerfit_solutions
from protein_detective.db import powerfit_solutions
In [16]:
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df = powerfit_solutions(conn)
df
df = powerfit_solutions(conn)
df
Out[16]:
| powerfit_run_id | structure | rank | cc | fishz | relz | translation | rotation | density_filter_id | af_id | pdb_id | pdb_file | uniprot_acc | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1 | A8MT69_4ne6_B2A | 1 | 0.456 | 0.492 | 11.071 | [227.18, 242.53, 211.83] | [0.0, -0.0, -1.0, 0.604, -0.797, 0.0, -0.797, ... | <NA> | None | 4NE6 | session1/single_chain/A8MT69_4ne6_B2A.pdb | A8MT69 |
| 1 | 1 | A8MT69_4drb_J2A | 1 | 0.444 | 0.477 | 10.588 | [227.18, 242.53, 214.9] | [0.797, -0.604, 0.0, 0.604, 0.797, 0.0, 0.0, 0... | <NA> | None | 4DRB | session1/single_chain/A8MT69_4drb_J2A.pdb | A8MT69 |
| 2 | 1 | A8MT69_4dra_E2A | 1 | 0.443 | 0.476 | 10.402 | [214.9, 187.27, 214.9] | [1.0, -0.0, 0.0, 0.0, -0.0, 1.0, -0.0, -1.0, -... | <NA> | None | 4DRA | session1/single_chain/A8MT69_4dra_E2A.pdb | A8MT69 |
| 3 | 1 | A8MT69_4e44_B2A | 1 | 0.440 | 0.472 | 10.099 | [224.11, 236.39, 227.18] | [1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0] | <NA> | None | 4E44 | session1/single_chain/A8MT69_4e44_B2A.pdb | A8MT69 |
| 4 | 1 | A8MT69_7xhn_X2A | 1 | 0.439 | 0.471 | 10.136 | [230.25, 242.53, 217.97] | [-1.0, 0.0, 0.0, 0.0, -1.0, 0.0, 0.0, 0.0, 1.0] | <NA> | None | 7XHN | session1/single_chain/A8MT69_7xhn_X2A.pdb | A8MT69 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 62752 | 1 | AF-A8MTY0-F1-model_v4 | 1463 | 0.095 | 0.095 | 5.424 | [168.85, 202.62, 236.39] | [0.0, 1.0, 0.0, 0.797, 0.0, -0.604, -0.604, 0.... | 1 | A8MTY0 | None | session1/density_filtered/AF-A8MTY0-F1-model_v... | A8MTY0 |
| 62753 | 1 | AF-A8MTY0-F1-model_v4 | 1462 | 0.095 | 0.095 | 5.425 | [122.8, 174.99, 147.36] | [0.797, 0.604, 0.0, 0.604, -0.797, 0.0, 0.0, 0... | 1 | A8MTY0 | None | session1/density_filtered/AF-A8MTY0-F1-model_v... | A8MTY0 |
| 62754 | 1 | AF-A8MTY0-F1-model_v4 | 1461 | 0.095 | 0.095 | 5.429 | [150.43, 211.83, 104.38] | [0.548, 0.548, 0.632, 0.184, -0.816, 0.548, 0.... | 1 | A8MTY0 | None | session1/density_filtered/AF-A8MTY0-F1-model_v... | A8MTY0 |
| 62755 | 1 | AF-A8MTY0-F1-model_v4 | 1460 | 0.095 | 0.096 | 5.437 | [224.11, 282.44, 150.43] | [0.0, 0.797, 0.604, -1.0, 0.0, -0.0, 0.0, -0.6... | 1 | A8MTY0 | None | session1/density_filtered/AF-A8MTY0-F1-model_v... | A8MTY0 |
| 62756 | 1 | AF-A8MTY0-F1-model_v4 | 1459 | 0.095 | 0.096 | 5.445 | [196.48, 196.48, 273.23] | [0.548, 0.548, 0.632, 0.184, -0.816, 0.548, 0.... | 1 | A8MTY0 | None | session1/density_filtered/AF-A8MTY0-F1-model_v... | A8MTY0 |
62757 rows × 13 columns
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df["cc"].plot(kind="hist", title="Histogram of CC Values", bins=40)
df["cc"].plot(kind="hist", title="Histogram of CC Values", bins=40)
Out[17]:
<Axes: title={'center': 'Histogram of CC Values'}, ylabel='Frequency'>
Show the top fitted models and their scores.
In [ ]:
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conn.execute("""
SELECT
f.* EXCLUDE (unfitted_model_file),
s.* EXCLUDE (pdb_file),
coalesce(f.unfitted_model_file, s.pdb_file) AS unfitted_model_file,
FROM fitted_models AS f
JOIN solutions AS s USING (powerfit_run_id, structure, rank)""").df()
conn.execute("""
SELECT
f.* EXCLUDE (unfitted_model_file),
s.* EXCLUDE (pdb_file),
coalesce(f.unfitted_model_file, s.pdb_file) AS unfitted_model_file,
FROM fitted_models AS f
JOIN solutions AS s USING (powerfit_run_id, structure, rank)""").df()
Out[ ]:
| powerfit_run_id | structure | rank | fitted_model_file | powerfit_run_id_1 | structure_1 | rank_1 | cc | fishz | relz | translation | rotation | density_filter_id | af_id | pdb_id | uniprot_acc | unfitted_model_file | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1 | A8MT69_4ne6_B2A | 1 | session1/powerfit/1/A8MT69_4ne6_B2A/fit_1.pdb | 1 | A8MT69_4ne6_B2A | 1 | 0.456 | 0.492 | 11.071 | [227.18, 242.53, 211.83] | [0.0, -0.0, -1.0, 0.604, -0.797, 0.0, -0.797, ... | <NA> | None | 4NE6 | A8MT69 | session1/single_chain/A8MT69_4ne6_B2A.pdb |
| 1 | 1 | A8MT69_4ne6_B2A | 2 | session1/powerfit/1/A8MT69_4ne6_B2A/fit_2.pdb | 1 | A8MT69_4ne6_B2A | 2 | 0.438 | 0.470 | 10.571 | [138.15, 153.5, 138.15] | [-0.797, 0.604, 0.0, 0.604, 0.797, 0.0, 0.0, 0... | <NA> | None | 4NE6 | A8MT69 | session1/single_chain/A8MT69_4ne6_B2A.pdb |
| 2 | 1 | A8MT69_4ne6_B2A | 3 | session1/powerfit/1/A8MT69_4ne6_B2A/fit_3.pdb | 1 | A8MT69_4ne6_B2A | 3 | 0.428 | 0.457 | 10.297 | [227.18, 138.15, 227.18] | [-0.0, 0.0, 1.0, 0.0, 1.0, 0.0, -1.0, 0.0, -0.0] | <NA> | None | 4NE6 | A8MT69 | session1/single_chain/A8MT69_4ne6_B2A.pdb |
| 3 | 1 | A8MT69_4ne6_B2A | 4 | session1/powerfit/1/A8MT69_4ne6_B2A/fit_4.pdb | 1 | A8MT69_4ne6_B2A | 4 | 0.407 | 0.432 | 9.720 | [276.3, 248.67, 153.5] | [0.0, 0.0, 1.0, 1.0, 0.0, 0.0, 0.0, 1.0, 0.0] | <NA> | None | 4NE6 | A8MT69 | session1/single_chain/A8MT69_4ne6_B2A.pdb |
| 4 | 1 | A8MT69_4ne6_B2A | 5 | session1/powerfit/1/A8MT69_4ne6_B2A/fit_5.pdb | 1 | A8MT69_4ne6_B2A | 5 | 0.399 | 0.422 | 9.498 | [184.2, 190.34, 205.69] | [0.816, 0.548, 0.184, -0.184, 0.548, -0.816, -... | <NA> | None | 4NE6 | A8MT69 | session1/single_chain/A8MT69_4ne6_B2A.pdb |
In [ ]:
Copied!