Use AlphaFold2

The input amino acid sequences for the structures you want to predict in FASTA format. For complexes simply enter the sequence for each chain separately.

Optionally provide a custom template structure for AlphaFold2 to use during prediction. Note that custom templates can only be used if you are predicting the structure of a single protein.

Allowed Types: fasta or a3m
Optionally provide a custom MSA (fasta or a3m format) for AlphaFold2 to use during the prediction. Note that custom MSAs can only be used if you are predicting the structure of a single protein. Make sure the first sequence in the MSA is the one you want to predict the structure of. Sequences will be truncated to the length of the first sequence (sequence that gets folded).

Check this option to utilize amber force fields to relax the predicted structure. This doesn't improve the prediction accuracy but does help remove otherwise distracting stereochemical violations.

Select the model you want to use to predict your structure. For monomers we recommend alphafold2_ptm, for complexes we recommend alphafold2_multimer_v3. If you leave this as auto alphafold2_ptm will be used for monomers and alphafold2_multimer_v3 will be used for complexes.

A template is an optional input structure that should be similar—but not identical—to the structure you are trying to predict. AlphaFold2 uses templates as a guide to improve predictions. Selecting "none" disables templates; selecting "pdb70" pulls a similar structure from pdb70. If you upload a custom template, this selection is ignored. Warning: We query a 3rd party service to perform template searches; if you do not wish to share your sequence, do not enable this option.

Choose the MSA database you want to use. Selecting "single_sequence" will result in the MSA containing only your target sequence. Note if you upload a custom MSA then your selection here will be ignored. In most cases mmseqs2_uniref_env tends to produce the best results. Warning: We query a 3rd party service to perform sequence searches, if you do not wish to share your sequence set this to "single_sequence".

This option applies to the input MSA. "unpaired_paired" = pair sequences from same species + unpaired MSA, "unpaired" = separate MSA for each chain, "paired" - only use paired sequences. Pairing the MSA can help AlphaFold2 create better predictions for complexes.

More recycling steps can improve accuracy but also increase prediction time. For smaller proteins and monomers we recommend 5 recycles; for bigger proteins we recommend 10. Maximum of 8 recycles for free users. Upgrade your plan to increase recycling values.

Ends the protein folding process if the improvement between recycling steps doesn't surpass the tolerance value. The tolerance is defined as the RMSD (difference in distance matrices, angstrom units) between recycles. If it drops below the specified value, the recycling will terminate. We recommend a tolerance of 0.3 for smaller proteins and 0.5 for larger proteins and complexes.

Runs the trunk multiple times with different MSA cluster centers (1=default, 8=casp14). More ensembling can improve quality but greatly increases runtime. Maximum of 1 ensemble for free users; contact support to raise this limit.

Check this option to enable "Training Mode" which activates drop out layers within the model. This can be used to force the model to create more diverse predictions.