@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.17s.
Visualizations and results¶
Original Structure Visualization¶
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@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.17s.
2kxoA_TEMP
Blue:3r9jC Red:2kxoA
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AlphaFold predictions¶
Best AF prediction to fold 1¶
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
Blue:ShallowMsa_053_unrelaxed_rank_001_alphafold2_ptm_model_2_seed_000 Red:3r9jC
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Best AF prediction to fold 2¶
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.16s.
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.16s.
2kxoA_TEMP
Blue:ShallowMsa_032_unrelaxed_rank_002_alphafold2_ptm_model_5_seed_000 Red:2kxoA
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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¶
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 545 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 566 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 545 atoms and 1 coordinate set(s) were parsed in 0.02s.
reference and target coordinate arrays must have same number of atoms ShallowMsa_064_2_TEMP
Blue:3r9jC Red:ShallowMsa_064_2
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
Best EsmFold prediction to fold 2¶
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.17s.
@> 524 atoms and 1 coordinate set(s) were parsed in 0.02s.
@> 1472 atoms and 10 coordinate set(s) were parsed in 0.16s.
@> 524 atoms and 1 coordinate set(s) were parsed in 0.02s.
reference and target coordinate arrays must have same number of atoms 0.61528 ShallowMsa_048_4_TEMP
Blue:2kxoA Red:ShallowMsa_048_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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 15536 | 3r9jC_2kxoA | ShallowMsa_048_4.pdb | 0.47871 | 0.61528 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15682 | 3r9jC_2kxoA | ShallowMsa_063_3.pdb | 0.47156 | 0.60160 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15690 | 3r9jC_2kxoA | ShallowMsa_063_9.pdb | 0.48518 | 0.59063 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15686 | 3r9jC_2kxoA | ShallowMsa_063_5.pdb | 0.49422 | 0.58042 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15689 | 3r9jC_2kxoA | ShallowMsa_063_8.pdb | 0.50147 | 0.57035 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15599 | 3r9jC_2kxoA | ShallowMsa_054_5.pdb | 0.49363 | 0.56908 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15688 | 3r9jC_2kxoA | ShallowMsa_063_6.pdb | 0.50077 | 0.56893 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15687 | 3r9jC_2kxoA | ShallowMsa_063_7.pdb | 0.50654 | 0.56016 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15533 | 3r9jC_2kxoA | ShallowMsa_048_6.pdb | 0.43770 | 0.56001 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15531 | 3r9jC_2kxoA | ShallowMsa_048_9.pdb | 0.52107 | 0.55348 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15539 | 3r9jC_2kxoA | ShallowMsa_048_3.pdb | 0.49405 | 0.54862 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15538 | 3r9jC_2kxoA | ShallowMsa_048_1.pdb | 0.45160 | 0.54796 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15597 | 3r9jC_2kxoA | ShallowMsa_054_6.pdb | 0.49761 | 0.52660 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15592 | 3r9jC_2kxoA | ShallowMsa_054_8.pdb | 0.48779 | 0.52649 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15684 | 3r9jC_2kxoA | ShallowMsa_063_0.pdb | 0.50101 | 0.52595 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15685 | 3r9jC_2kxoA | ShallowMsa_063_4.pdb | 0.49695 | 0.52429 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15683 | 3r9jC_2kxoA | ShallowMsa_063_1.pdb | 0.49459 | 0.52260 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15598 | 3r9jC_2kxoA | ShallowMsa_054_7.pdb | 0.48354 | 0.51440 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15540 | 3r9jC_2kxoA | ShallowMsa_048_2.pdb | 0.49958 | 0.50860 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15537 | 3r9jC_2kxoA | ShallowMsa_048_0.pdb | 0.49432 | 0.50684 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15593 | 3r9jC_2kxoA | ShallowMsa_054_0.pdb | 0.47024 | 0.50605 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15591 | 3r9jC_2kxoA | ShallowMsa_054_9.pdb | 0.47822 | 0.49737 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15532 | 3r9jC_2kxoA | ShallowMsa_048_8.pdb | 0.51104 | 0.49413 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15594 | 3r9jC_2kxoA | ShallowMsa_054_1.pdb | 0.46458 | 0.47816 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15534 | 3r9jC_2kxoA | ShallowMsa_048_7.pdb | 0.45943 | 0.46651 | 048 | 0.484980 | 0.516179 | 10 | 0 | 1 | 0 | 1 |
| 15600 | 3r9jC_2kxoA | ShallowMsa_054_4.pdb | 0.45969 | 0.46651 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15596 | 3r9jC_2kxoA | ShallowMsa_054_2.pdb | 0.46739 | 0.45337 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15681 | 3r9jC_2kxoA | ShallowMsa_063_2.pdb | 0.40292 | 0.43712 | 063 | 0.485521 | 0.548205 | 10 | 0 | 1 | 0 | 1 |
| 15595 | 3r9jC_2kxoA | ShallowMsa_054_3.pdb | 0.46081 | 0.38543 | 054 | 0.476350 | 0.492346 | 10 | 0 | 1 | 0 | 1 |
| 15535 | 3r9jC_2kxoA | ShallowMsa_048_5.pdb | 0.50230 | 0.36036 | 048 | 0.484980 | 0.516179 | 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)
