@> 5385 atoms and 1 coordinate set(s) were parsed in 0.19s.

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.15s.

Visualizations and results¶

Original Structure Visualization¶

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@> 5385 atoms and 1 coordinate set(s) were parsed in 0.20s.

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.15s.

3o44A_TEMP

Blue:1xezA
Red:3o44A

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AlphaFold predictions¶

Best AF prediction to fold 1¶

@> 5221 atoms and 1 coordinate set(s) were parsed in 0.18s.

@> 5385 atoms and 1 coordinate set(s) were parsed in 0.18s.

Blue:ShallowMsa_002_unrelaxed_rank_002_alphafold2_ptm_model_3_seed_000
Red:1xezA

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Best AF prediction to fold 2¶

@> 5221 atoms and 1 coordinate set(s) were parsed in 0.19s.

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.17s.

@> 5221 atoms and 1 coordinate set(s) were parsed in 0.17s.

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.16s.

3o44A_TEMP

Blue:ShallowMsa_001_unrelaxed_rank_003_alphafold2_ptm_model_1_seed_000
Red:3o44A

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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¶

single positional indexer is out-of-bounds
name 'max_esm_pdb1' is not defined

Best EsmFold prediction to fold 2¶

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.18s.

@> 5183 atoms and 1 coordinate set(s) were parsed in 0.19s.

@> 4522 atoms and 1 coordinate set(s) were parsed in 0.15s.

reference and target coordinate arrays must have same number of atoms
0.72874

@> 5183 atoms and 1 coordinate set(s) were parsed in 0.17s.

ShallowMsa_001_4_TEMP

Blue:3o44A
Red:ShallowMsa_001_4

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
3958 1xezA_3o44A ShallowMsa_001_4.pdb 0.53491 0.72874 001 0.515671 0.624674 10 0 1 0 1
3955 1xezA_3o44A ShallowMsa_001_3.pdb 0.53952 0.70580 001 0.515671 0.624674 10 0 1 0 1
3960 1xezA_3o44A ShallowMsa_001_7.pdb 0.50867 0.68297 001 0.515671 0.624674 10 0 1 0 1
3948 1xezA_3o44A ShallowMsa_000_7.pdb 0.50806 0.67528 000 0.549002 0.550545 10 0 1 0 1
3975 1xezA_3o44A ShallowMsa_003_1.pdb 0.50806 0.67528 003 0.514761 0.542151 10 0 1 0 1
3973 1xezA_3o44A ShallowMsa_002_8.pdb 0.50806 0.67528 002 0.507196 0.551468 10 0 1 0 1
3961 1xezA_3o44A ShallowMsa_001_6.pdb 0.50806 0.67528 001 0.515671 0.624674 10 0 1 0 1
3956 1xezA_3o44A ShallowMsa_001_1.pdb 0.52010 0.63122 001 0.515671 0.624674 10 0 1 0 1
3959 1xezA_3o44A ShallowMsa_001_5.pdb 0.49776 0.59621 001 0.515671 0.624674 10 0 1 0 1
3979 1xezA_3o44A ShallowMsa_003_7.pdb 0.55675 0.59118 003 0.514761 0.542151 10 0 1 0 1
3962 1xezA_3o44A ShallowMsa_001_8.pdb 0.52193 0.57805 001 0.515671 0.624674 10 0 1 0 1
3964 1xezA_3o44A ShallowMsa_002_3.pdb 0.61011 0.56572 002 0.507196 0.551468 10 0 1 0 1
3966 1xezA_3o44A ShallowMsa_002_0.pdb 0.48607 0.56551 002 0.507196 0.551468 10 0 1 0 1
3967 1xezA_3o44A ShallowMsa_002_1.pdb 0.53000 0.56495 002 0.507196 0.551468 10 0 1 0 1
3946 1xezA_3o44A ShallowMsa_000_2.pdb 0.54821 0.56310 000 0.549002 0.550545 10 0 1 0 1
3963 1xezA_3o44A ShallowMsa_001_9.pdb 0.49890 0.56272 001 0.515671 0.624674 10 0 1 0 1
3950 1xezA_3o44A ShallowMsa_000_4.pdb 0.57678 0.56228 000 0.549002 0.550545 10 0 1 0 1
3951 1xezA_3o44A ShallowMsa_000_5.pdb 0.56802 0.56031 000 0.549002 0.550545 10 0 1 0 1
3952 1xezA_3o44A ShallowMsa_000_8.pdb 0.60670 0.56029 000 0.549002 0.550545 10 0 1 0 1
3982 1xezA_3o44A ShallowMsa_003_9.pdb 0.53812 0.55561 003 0.514761 0.542151 10 0 1 0 1
3953 1xezA_3o44A ShallowMsa_000_9.pdb 0.55336 0.55213 000 0.549002 0.550545 10 0 1 0 1
3947 1xezA_3o44A ShallowMsa_000_3.pdb 0.61287 0.54895 000 0.549002 0.550545 10 0 1 0 1
3977 1xezA_3o44A ShallowMsa_003_2.pdb 0.52505 0.54840 003 0.514761 0.542151 10 0 1 0 1
3945 1xezA_3o44A ShallowMsa_000_0.pdb 0.56432 0.54400 000 0.549002 0.550545 10 0 1 0 1
3957 1xezA_3o44A ShallowMsa_001_0.pdb 0.53736 0.54341 001 0.515671 0.624674 10 0 1 0 1
3981 1xezA_3o44A ShallowMsa_003_4.pdb 0.54389 0.54293 003 0.514761 0.542151 10 0 1 0 1
3954 1xezA_3o44A ShallowMsa_001_2.pdb 0.48950 0.54234 001 0.515671 0.624674 10 0 1 0 1
3978 1xezA_3o44A ShallowMsa_003_6.pdb 0.55068 0.53891 003 0.514761 0.542151 10 0 1 0 1
3968 1xezA_3o44A ShallowMsa_002_5.pdb 0.46384 0.53561 002 0.507196 0.551468 10 0 1 0 1
3980 1xezA_3o44A ShallowMsa_003_5.pdb 0.50884 0.53088 003 0.514761 0.542151 10 0 1 0 1
3972 1xezA_3o44A ShallowMsa_002_9.pdb 0.50880 0.53062 002 0.507196 0.551468 10 0 1 0 1
3969 1xezA_3o44A ShallowMsa_002_4.pdb 0.51750 0.52971 002 0.507196 0.551468 10 0 1 0 1
3976 1xezA_3o44A ShallowMsa_003_3.pdb 0.48893 0.52932 003 0.514761 0.542151 10 0 1 0 1
3971 1xezA_3o44A ShallowMsa_002_7.pdb 0.46566 0.52895 002 0.507196 0.551468 10 0 1 0 1
3970 1xezA_3o44A ShallowMsa_002_6.pdb 0.49264 0.52882 002 0.507196 0.551468 10 0 1 0 1
3965 1xezA_3o44A ShallowMsa_002_2.pdb 0.48928 0.48951 002 0.507196 0.551468 10 0 1 0 1
3949 1xezA_3o44A ShallowMsa_000_6.pdb 0.49020 0.48950 000 0.549002 0.550545 10 0 1 0 1
3974 1xezA_3o44A ShallowMsa_003_0.pdb 0.46846 0.47696 003 0.514761 0.542151 10 0 1 0 1
3944 1xezA_3o44A ShallowMsa_000_1.pdb 0.46150 0.44961 000 0.549002 0.550545 10 0 1 0 1
3983 1xezA_3o44A ShallowMsa_003_8.pdb 0.45883 0.43204 003 0.514761 0.542151 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)
No description has been provided for this image
No description has been provided for this image