@> 933 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
Visualizations and results¶
Original Structure Visualization¶
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@> 933 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
4qhfA_TEMP Blue:4qhhA Red:4qhfA
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AlphaFold predictions¶
Best AF prediction to fold 1¶
No max_af_pdb1
Best AF prediction to fold 2¶
@> 906 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 906 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
4qhfA_TEMP
Blue:ShallowMsa_002_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000 Red:4qhfA
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EsmFold Prediction¶
Out[10]:
| fold_pair | fold | TMscore_fold1 | TMscore_fold2 | cluster_num | TM_mean_cluster_pdb1 | TM_mean_cluster_pdb2 | sample_count | is_fold_1 | is_fold_2 | cluster_fold_1 | cluster_fold_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 1dzlA_5keqF | ShallowMsa_000_1.pdb | 0.21478 | 0.22071 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 1 | 1dzlA_5keqF | ShallowMsa_000_0.pdb | 0.23730 | 0.24378 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 2 | 1dzlA_5keqF | ShallowMsa_000_2.pdb | 0.38172 | 0.36978 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 3 | 1dzlA_5keqF | ShallowMsa_000_3.pdb | 0.38407 | 0.38314 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
| 4 | 1dzlA_5keqF | ShallowMsa_000_7.pdb | 0.18823 | 0.17477 | 000 | 0.281451 | 0.2755 | 10 | 1 | 0 | 1 | 0 |
Best EsmFold prediction to fold 1¶
name 'pdb_file1_' is not defined name 'pdb_file1_' is not defined
Best EsmFold prediction to fold 2¶
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 906 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 979 atoms and 1 coordinate set(s) were parsed in 0.03s.
@> 906 atoms and 1 coordinate set(s) were parsed in 0.03s.
reference and target coordinate arrays must have same number of atoms 0.93668 ShallowMsa_002_4_TEMP
Blue:4qhfA Red:ShallowMsa_002_4
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Out[13]:
| fold_pair | fold | TMscore_fold1 | TMscore_fold2 | cluster_num | TM_mean_cluster_pdb1 | TM_mean_cluster_pdb2 | sample_count | is_fold_1 | is_fold_2 | cluster_fold_1 | cluster_fold_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 19782 | 4qhhA_4qhfA | ShallowMsa_002_4.pdb | 0.65073 | 0.93668 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19804 | 4qhhA_4qhfA | ShallowMsa_004_1.pdb | 0.65073 | 0.93668 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19788 | 4qhhA_4qhfA | ShallowMsa_003_1.pdb | 0.65073 | 0.93668 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19777 | 4qhhA_4qhfA | ShallowMsa_002_3.pdb | 0.65073 | 0.93668 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19786 | 4qhhA_4qhfA | ShallowMsa_002_8.pdb | 0.65111 | 0.92766 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19780 | 4qhhA_4qhfA | ShallowMsa_002_1.pdb | 0.60345 | 0.82191 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19784 | 4qhhA_4qhfA | ShallowMsa_002_7.pdb | 0.60550 | 0.80396 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19791 | 4qhhA_4qhfA | ShallowMsa_003_6.pdb | 0.58735 | 0.80120 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19783 | 4qhhA_4qhfA | ShallowMsa_002_6.pdb | 0.60751 | 0.79543 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19789 | 4qhhA_4qhfA | ShallowMsa_003_3.pdb | 0.57108 | 0.79440 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19796 | 4qhhA_4qhfA | ShallowMsa_003_8.pdb | 0.56900 | 0.79006 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19770 | 4qhhA_4qhfA | ShallowMsa_001_0.pdb | 0.57243 | 0.78066 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19776 | 4qhhA_4qhfA | ShallowMsa_001_9.pdb | 0.56861 | 0.76387 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19790 | 4qhhA_4qhfA | ShallowMsa_003_2.pdb | 0.58407 | 0.76204 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19768 | 4qhhA_4qhfA | ShallowMsa_001_3.pdb | 0.57330 | 0.74187 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19767 | 4qhhA_4qhfA | ShallowMsa_001_2.pdb | 0.53211 | 0.74150 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19802 | 4qhhA_4qhfA | ShallowMsa_004_2.pdb | 0.55014 | 0.73280 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19771 | 4qhhA_4qhfA | ShallowMsa_001_4.pdb | 0.51130 | 0.72616 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19803 | 4qhhA_4qhfA | ShallowMsa_004_0.pdb | 0.57661 | 0.71406 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19769 | 4qhhA_4qhfA | ShallowMsa_001_1.pdb | 0.55329 | 0.70875 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19781 | 4qhhA_4qhfA | ShallowMsa_002_5.pdb | 0.59793 | 0.70825 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19798 | 4qhhA_4qhfA | ShallowMsa_004_4.pdb | 0.56663 | 0.70825 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19799 | 4qhhA_4qhfA | ShallowMsa_004_6.pdb | 0.54318 | 0.69976 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19778 | 4qhhA_4qhfA | ShallowMsa_002_2.pdb | 0.58765 | 0.69641 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19785 | 4qhhA_4qhfA | ShallowMsa_002_9.pdb | 0.61041 | 0.69387 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19816 | 4qhhA_4qhfA | ShallowMsa_005_8.pdb | 0.52982 | 0.69355 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19815 | 4qhhA_4qhfA | ShallowMsa_005_9.pdb | 0.57871 | 0.69233 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19779 | 4qhhA_4qhfA | ShallowMsa_002_0.pdb | 0.60632 | 0.68685 | 002 | 0.617134 | 0.800770 | 10 | 0 | 1 | 0 | 1 |
| 19809 | 4qhhA_4qhfA | ShallowMsa_005_5.pdb | 0.52304 | 0.68437 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19797 | 4qhhA_4qhfA | ShallowMsa_004_5.pdb | 0.54299 | 0.68383 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19800 | 4qhhA_4qhfA | ShallowMsa_004_7.pdb | 0.54108 | 0.67724 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19812 | 4qhhA_4qhfA | ShallowMsa_005_1.pdb | 0.53273 | 0.67689 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19811 | 4qhhA_4qhfA | ShallowMsa_005_0.pdb | 0.54031 | 0.66211 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19807 | 4qhhA_4qhfA | ShallowMsa_005_6.pdb | 0.53626 | 0.66210 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19810 | 4qhhA_4qhfA | ShallowMsa_005_4.pdb | 0.54563 | 0.66098 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19801 | 4qhhA_4qhfA | ShallowMsa_004_3.pdb | 0.53511 | 0.65965 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19814 | 4qhhA_4qhfA | ShallowMsa_005_2.pdb | 0.54290 | 0.65665 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19806 | 4qhhA_4qhfA | ShallowMsa_004_8.pdb | 0.49309 | 0.65590 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19808 | 4qhhA_4qhfA | ShallowMsa_005_7.pdb | 0.52808 | 0.65538 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19813 | 4qhhA_4qhfA | ShallowMsa_005_3.pdb | 0.51319 | 0.62361 | 005 | 0.537067 | 0.666797 | 10 | 0 | 1 | 0 | 1 |
| 19805 | 4qhhA_4qhfA | ShallowMsa_004_9.pdb | 0.47540 | 0.61877 | 004 | 0.547496 | 0.708694 | 10 | 0 | 1 | 0 | 1 |
| 19775 | 4qhhA_4qhfA | ShallowMsa_001_8.pdb | 0.58889 | 0.59577 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19792 | 4qhhA_4qhfA | ShallowMsa_003_7.pdb | 0.57760 | 0.58911 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19772 | 4qhhA_4qhfA | ShallowMsa_001_5.pdb | 0.59180 | 0.58862 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19793 | 4qhhA_4qhfA | ShallowMsa_003_5.pdb | 0.58914 | 0.58739 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19787 | 4qhhA_4qhfA | ShallowMsa_003_0.pdb | 0.58931 | 0.58359 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19794 | 4qhhA_4qhfA | ShallowMsa_003_4.pdb | 0.59738 | 0.57971 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19795 | 4qhhA_4qhfA | ShallowMsa_003_9.pdb | 0.58767 | 0.57632 | 003 | 0.590333 | 0.700050 | 10 | 0 | 1 | 0 | 1 |
| 19773 | 4qhhA_4qhfA | ShallowMsa_001_7.pdb | 0.53295 | 0.53630 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
| 19774 | 4qhhA_4qhfA | ShallowMsa_001_6.pdb | 0.52243 | 0.52298 | 001 | 0.554711 | 0.670648 | 10 | 0 | 1 | 0 | 1 |
Contact maps Msa Transformers¶
Out[15]:
array(['1qb3A_3qy2A', '3l5nB_2a73B', '5l35G_5l35D', '4ydqB_4twaA',
'2mwfA_2nntA', '1qlnA_1h38D', '1xezA_3o44A', '1zk9A_3jv6A',
'1xjuB_1xjtA', '3meeA_4b3oB', '3r9jC_2kxoA', '5f5rB_5f3kA',
'1nqjB_1nqdA', '4yhdG_7ahlE', '1mnmD_1mnmC', '2bzyB_2lqwA',
'3lowA_3m1bF', '1iytA_2naoF', '2kb8A_6vw2A', '5et5A_3ifaA',
'1nocA_1qomB', '4o01D_4o0pA', '3v0tA_3uyiA', '4q79F_4uv2D',
'2uy7D_5fluE', '5c1vB_5c1vA', '2k42A_1ceeB', '2lelA_2k0qA',
'1miqB_1qs8B', '3t5oA_4a5wB', '6c6sD_2ougC', '3lqcA_1xntA',
'3mkoA_5ineA', '5jytA_2qkeE', '4dxrA_4dxtA', '2kkwA_2n0aD',
'5c3iF_3kuyA', '5tpnA_1g2cF', '3j7vG_3j7wB', '1svfC_4wsgC',
'5jztG_5jzhA', '5bmyA_5b3zA', '2z9oB_1repC', '2n54B_2hdmA',
'3g0hA_3ewsB', '1rk4B_1k0nA', '1kctA_3t1pA', '2c1vB_2c1uC',
'2lv1A_6lniA', '4pyjA_4pyiA', '2qqjA_4qdsA', '1xtgB_3j97M',
'4n9wA_4nc9C', '2lepA_4hddA', '5lj3M_3tp2A', '5i2sA_5i2mA',
'5ly6B_5aoeB', '4tsyD_3zwgN', '3m7pA_3ejhA', '1eboE_5fhcJ',
'2jmrA_4j3oF', '2namA_1uxmK', '4qhhA_4qhfA', '1dzlA_5keqF',
'4rmbB_4rmbA', '2pbkB_3njqA', '4xwsD_4y0mJ', '2h44A_1rkpA',
'5wrgC_1wyyB', '1jfkA_2nxqB', '3kdsG_2ce7C', '3hdfA_3hdeA',
'3ztjE_5hmgA', '1x0gD_1x0gA', '3l9qB_4rr2D', '1nrjB_2gedB',
'4rwqB_4rwnA', '2p3vD_2p3vA', '4h2aA_3j9cA', '5hk5H_4jphB',
'4zrbH_4zrbC', '2vfxL_3gmhL', '4gqcB_4gqcC'], dtype=object)
