@> 1077 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
Visualizations and results¶
Original Structure Visualization¶
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
@> 1077 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
5fluE_TEMP Blue:2uy7D Red:5fluE
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
AlphaFold predictions¶
Best AF prediction to fold 1¶
@> 1108 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1077 atoms and 1 coordinate set(s) were parsed in 0.04s.
Blue:ShallowMsa_040_unrelaxed_rank_005_alphafold2_ptm_model_1_seed_000 Red:2uy7D
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
Best AF prediction to fold 2¶
@> 1108 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1108 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
5fluE_TEMP Blue:ShallowMsa_045_unrelaxed_rank_001_alphafold2_ptm_model_5_seed_000 Red:5fluE
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¶
@> 1077 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1108 atoms and 1 coordinate set(s) were parsed in 0.04s.
Blue:2uy7D Red:ShallowMsa_034_4
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
Best EsmFold prediction to fold 2¶
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1106 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1164 atoms and 1 coordinate set(s) were parsed in 0.04s.
@> 1106 atoms and 1 coordinate set(s) were parsed in 0.04s.
reference and target coordinate arrays must have same number of atoms 0.84157 ShallowMsa_025_3_TEMP
Blue:5fluE Red:ShallowMsa_025_3
3Dmol.js failed to load for some reason. Please check your browser console for error messages.
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 9532 | 2uy7D_5fluE | ShallowMsa_025_3.pdb | 0.74782 | 0.84157 | 025 | 0.768041 | 0.817412 | 10 | 0 | 1 | 0 | 1 |
| 9604 | 2uy7D_5fluE | ShallowMsa_032_4.pdb | 0.73600 | 0.83744 | 032 | 0.709248 | 0.773391 | 10 | 0 | 1 | 0 | 1 |
| 9539 | 2uy7D_5fluE | ShallowMsa_025_7.pdb | 0.76274 | 0.83732 | 025 | 0.768041 | 0.817412 | 10 | 0 | 1 | 0 | 1 |
| 9418 | 2uy7D_5fluE | ShallowMsa_013_4.pdb | 0.77140 | 0.83197 | 013 | 0.691659 | 0.739857 | 10 | 0 | 1 | 0 | 1 |
| 9380 | 2uy7D_5fluE | ShallowMsa_009_7.pdb | 0.77140 | 0.83197 | 009 | 0.706873 | 0.740354 | 10 | 0 | 1 | 0 | 1 |
| ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... | ... |
| 9479 | 2uy7D_5fluE | ShallowMsa_019_4.pdb | 0.64632 | 0.65851 | 019 | 0.680367 | 0.735156 | 10 | 0 | 1 | 0 | 1 |
| 9599 | 2uy7D_5fluE | ShallowMsa_031_2.pdb | 0.63839 | 0.65379 | 031 | 0.657326 | 0.690180 | 10 | 0 | 1 | 0 | 1 |
| 9442 | 2uy7D_5fluE | ShallowMsa_016_9.pdb | 0.59180 | 0.62194 | 016 | 0.718308 | 0.764983 | 10 | 0 | 1 | 0 | 1 |
| 9470 | 2uy7D_5fluE | ShallowMsa_018_9.pdb | 0.59194 | 0.61830 | 018 | 0.659277 | 0.706241 | 10 | 0 | 1 | 0 | 1 |
| 9659 | 2uy7D_5fluE | ShallowMsa_037_4.pdb | 0.57450 | 0.59871 | 037 | 0.656775 | 0.700031 | 10 | 0 | 1 | 0 | 1 |
440 rows × 12 columns
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)
