Iedb Prediction Tools#

Configuration File: iedb_prediction_tools.json Tool Type: Local Tools Count: 4

This page contains all tools defined in the iedb_prediction_tools.json configuration file.

Available Tools#

IEDB_predict_antigen_processing (Type: IEDBPredictionTool)#

Predict MHC class I antigen processing using the IEDB next-generation tools API (https://api-next…

IEDB_predict_antigen_processing tool specification

Tool Information:

  • Name: IEDB_predict_antigen_processing

  • Type: IEDBPredictionTool

  • Description: Predict MHC class I antigen processing using the IEDB next-generation tools API (https://api-nextgen-tools.iedb.org). Unlike raw binding prediction, this runs the NetCTLpan processing predictor alongside an MHC-I binding predictor, chaining proteasomal cleavage + TAP transport + MHC-I binding into a combined score that identifies peptides likely to be naturally processed and presented to CD8+ T cells. Returns one row per peptide with cleavage_prediction_score, tap_prediction_score, mhc_prediction and combined_prediction_score (sorted highest first), alongside the binding method’s own IC50/score and percentile columns. Use for neoantigen and epitope prioritization beyond binding affinity. Sequences of 20 or more residues are recommended, since cleavage prediction needs flanking context. No authentication required.

Parameters:

  • sequence (string) (required) Protein sequence (single-letter amino acids), e.g. ‘SLYNTVATLYCVHQRIDVKQNTLKLATGGKS’. 20+ residues recommended. Aliases: sequence_text.

  • sequence_text (string) (optional) Alias for sequence.

  • allele (string) (optional) MHC class I allele, validated upstream against the MHC Restriction Ontology. Human: ‘HLA-A*02:01’, ‘HLA-B*07:02’. Mouse: ‘H2-Kd’ (the legacy ‘H-2-Kd’ spelling is accepted and translated). Default: HLA-A*02:01

  • method (string) (optional) MHC-I binding method used in the chain: ‘netmhcpan’ (default), ‘netmhcpan_ba’, ‘netmhcpan_el’, ‘ann’, ‘smm’, ‘smmpmbec’, ‘comblib_sidney2008’, ‘consensus’.

  • length (integer) (optional) Peptide length (8-15 for MHC-I, typically 9).

Example Usage:

query = {
    "name": "IEDB_predict_antigen_processing",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

IEDB_predict_bcell_epitopes (Type: IEDBPredictionTool)#

Predict linear B-cell (antibody) epitopes along a protein sequence using the IEDB B-cell tool (de…

IEDB_predict_bcell_epitopes tool specification

Tool Information:

  • Name: IEDB_predict_bcell_epitopes

  • Type: IEDBPredictionTool

  • Description: Predict linear B-cell (antibody) epitopes along a protein sequence using the IEDB B-cell tool (default BepiPred). Scores every residue and returns the contiguous regions predicted to be antibody-accessible epitopes, plus the per-residue scores. Use for vaccine antigen design and antibody target selection. Example: a viral surface protein sequence returns its predicted surface-exposed epitope stretches.

Parameters:

  • sequence (string) (required) Protein amino-acid sequence (single-letter codes), e.g. an antigen of interest.

  • method ([‘string’, ‘null’]) (optional) Prediction method: ‘Bepipred’ (default, BepiPred-2.0), ‘Emini’ (surface accessibility), ‘Kolaskar-Tongaonkar’ (antigenicity), ‘Parker’ (hydrophilicity), ‘Chou-Fasman’ (beta-turn).

Example Usage:

query = {
    "name": "IEDB_predict_bcell_epitopes",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

IEDB_predict_mhci_binding (Type: IEDBPredictionTool)#

Predict MHC class I peptide binding using NetMHCpan via the IEDB next-generation tools API (https…

IEDB_predict_mhci_binding tool specification

Tool Information:

  • Name: IEDB_predict_mhci_binding

  • Type: IEDBPredictionTool

  • Description: Predict MHC class I peptide binding using NetMHCpan via the IEDB next-generation tools API (https://api-nextgen-tools.iedb.org). Given a protein sequence and HLA allele, predicts which peptides will bind and be presented on the cell surface. Returns one row per scored peptide with the method’s own score/IC50 and percentile columns, plus a uniform ‘percentile_rank’ (lower = stronger binding), sorted strongest first. Essential for vaccine design, neoantigen prediction, and epitope mapping. Supports human HLA-A/B/C and mouse H2 alleles. The prediction runs asynchronously upstream and typically returns within about 15 seconds.

Parameters:

  • sequence (string) (required) Protein sequence (amino acid letters, e.g., ‘TYQRTRALVFQRTRALKMFAL’). Multiple peptides can be concatenated. A FASTA block (starting with ‘>’) is also accepted.

  • allele (string) (optional) MHC allele name, validated upstream against the MHC Restriction Ontology. Human: ‘HLA-A*02:01’, ‘HLA-B*07:02’. Mouse: ‘H2-Kd’, ‘H2-Db’ (the legacy ‘H-2-Kd’ spelling is accepted and translated). Comma-separate for several alleles. Default: HLA-A*02:01

  • method (string) (optional) Prediction method: ‘netmhcpan_el’ (recommended, eluted ligand), ‘netmhcpan_ba’ (binding affinity), ‘netmhcpan’, ‘ann’, ‘smm’, ‘smmpmbec’, ‘comblib_sidney2008’, ‘consensus’, ‘mhcflurry’, ‘mhcnp’, ‘pickpocket’

  • length (integer) (optional) Peptide length (8-15 for MHC-I, typically 9)

Example Usage:

query = {
    "name": "IEDB_predict_mhci_binding",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)

IEDB_predict_mhcii_binding (Type: IEDBPredictionTool)#

Predict MHC class II peptide binding using NetMHCIIpan via the IEDB next-generation tools API (ht…

IEDB_predict_mhcii_binding tool specification

Tool Information:

  • Name: IEDB_predict_mhcii_binding

  • Type: IEDBPredictionTool

  • Description: Predict MHC class II peptide binding using NetMHCIIpan via the IEDB next-generation tools API (https://api-nextgen-tools.iedb.org). Predicts CD4+ T helper cell epitopes. Given a protein sequence and HLA-DR/DP/DQ allele, returns one row per scored sliding-window peptide with the method’s own core/score/percentile columns plus a uniform ‘percentile_rank’ (lower = stronger binding), sorted strongest first. Essential for vaccine design (helper epitopes) and autoimmunity research. The prediction runs asynchronously upstream and typically returns within about 15 seconds.

Parameters:

  • sequence (string) (required) Protein sequence (amino acid letters). A FASTA block (starting with ‘>’) is also accepted.

  • allele (string) (optional) MHC-II allele, validated upstream against the MHC Restriction Ontology. Examples: ‘HLA-DRB1*01:01’, ‘HLA-DRB1*15:01’. Comma-separate for several alleles. Default: HLA-DRB1*01:01

  • method (string) (optional) Prediction method: ‘netmhciipan_el’ (recommended), ‘netmhciipan_ba’, ‘nn_align’, ‘smm_align’, ‘comblib’, ‘tepitope’, ‘consensus’

  • length ([‘integer’, ‘null’]) (optional) Sliding-window peptide length scored within ‘sequence’ (11-30, default 15). Cannot exceed the sequence length; omit to use 15, or the sequence’s own length when that is shorter.

Example Usage:

query = {
    "name": "IEDB_predict_mhcii_binding",
    "arguments": {
        "sequence": "example_value"
    }
}
result = tu.run(query)