Predict a pair or batch
Open Pairwise Interaction Prediction and choose Single pair or Batch CSV. Enter the sequences or upload a CSV file, correct any input errors, and review the truncation limits before submitting. Save the private job link. Interpret the probability together with the threshold and model version.
Retrieve candidates
Open Interaction Partner Sequence Prediction. Specify whether the input protein is human or viral, enter one sequence, and select 5, 10, or 20 candidates. After submission, the model predicts a partner embedding and returns the closest natural sequences with similarity scores and source information.
Prepare input
Each sequence field accepts plain sequence text or one FASTA record. A batch CSV contains one protein pair per row and must use the specified column names. All rows are checked; an invalid row prevents submission of the entire batch.
Long sequences
ESM processes at most 1,024 tokens in total, including BOS/EOS (normally up to 1,022 residues); AAindex uses the first 100 residues. Sequences of up to 10,000 residues can be submitted, but residues beyond these encoding limits do not contribute to the corresponding features.
Queue and return
A single CPU process runs tasks in submission order. Closing the page does not cancel an accepted task. Use the complete private job link to return before expiry, and keep the link confidential.
Shared submission limits
Each IP address may have up to two unfinished jobs and ten accepted submissions in any one-hour period. Users who share an external IP address share these limits.
CSV exports
In CSV exports, text identifiers that could be interpreted as spreadsheet formulas are prefixed with an apostrophe. JSON exports retain the original identifiers.
Fix errors
For input errors, correct the indicated row and field. If the queue is full, wait before submitting again. Review the error code before resubmitting a failed task. Expired results must be recomputed from the original sequences.
FASTA / CSV
Whitespace and alignment gaps are removed, letters are converted to uppercase, and a single terminal * is removed.
>format_example ACDEFGHIKLMNPQRSTVWY
pair_id,human_seq,viral_seq format_1,ACDEFGHIKLMNPQRSTVWY,MKTAYIAKQRQISFVKSHFS