This walkthrough uses ESMFold2 to predict a protein structure from one sequence. It demonstrates the submission and review process; it is not a benchmark or a claim about a particular biological target.
Before you begin
- Create an account or sign in.
- Have credits available through your account or team. Review credit estimates before submitting.
- Use a protein sequence you are permitted to submit. Keep a copy of the exact sequence and any scientific assumptions.
For a small example, the following is the 76-residue human ubiquitin sequence. Paste the amino-acid sequence into a protein-sequence entry on the tool form; use the form’s separate name field if one is provided.
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG
This example is a single protein chain. Do not add a FASTA header to a field that expects only the sequence.
Choose the service
Open ESMFold2. Read the overview and check the current form instructions. For your own research, choose a method based on the molecular system rather than simply repeating this example; the structure prediction guide explains the choices.
Configure and review
- Add one protein-sequence entity and paste the example sequence.
- Keep the default settings for this first run, after reading their descriptions. Do not add ligands, additional chains, or restraints for this monomer example.
- Add a recognizable job note such as
First structure prediction — ubiquitin. - Review the inputs and estimated credits, then submit the job once.
Submitting executes a computation and can consume credits. An estimate is not a guaranteed final charge. If the submission response is uncertain, check your workspace before submitting again.
Follow the job
Open Workspace and find the submission in Past Jobs. Pending jobs have not started execution; running jobs are still processing. Wait for completion before interpreting results. If the job fails, inspect its error instead of repeatedly resubmitting unchanged inputs.
You can browse other tools while the job runs. See Jobs and results for states, organization, and troubleshooting.
Inspect the result
Open the job page and review the available structures, tables, plots, and files. Exact outputs depend on the tool and version.
- Confirm that the predicted chain corresponds to the submitted sequence.
- Inspect confidence along the chain, not just a single average score.
- Review uncertain termini, loops, and domains before using coordinates downstream.
- Download the structure and relevant output tables together with the job ID and settings.
For this known, compact protein, an experimental ubiquitin structure can provide a useful comparison. A similar-looking fold does not validate all models or imply that every predicted contact is correct.
Choose a next step
Use the viewer to inspect the structure, learn how to prepare inputs, or compare methods in Structure prediction. For complexes, ligand interactions, or flexible proteins, define that larger question before choosing the next calculation.