ProteinIQ
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ProteinIQ

Send only your best peptides to the lab

Design peptide binders, check cleavage and immunogenicity risk, and model how they sit on the target before synthesis.

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HLA-A2 with Tel1p peptide, a Boltz-2 result on ProteinIQ
  1. Candidate generation

    Generate or extend peptide sequences from target context while keeping each design method’s native ranking and files.

    PepMimic

    PepMimic

    Peptide binder design through binding interface mimicry with a latent diffusion model

    binder-designai-powered+4
    BoltzProt-1

    BoltzProt-1

    Protein, peptide, nanobody and antibody binder design.

    protein-designbinder-design+3
    BoltzGen

    BoltzGen

    Design protein, peptide, and nanobody binders against protein or small-molecule targets.

    binder-designai-powered+5
  2. Sequence and proteolysis review

    Calculate baseline sequence properties and identify cleavage liabilities before advancing candidates.

    Peptide mass calculator

    Peptide mass calculator

    In-silico proteolytic digestion with peptide mass calculation for mass spectrometry experiment planning.

    protein-analysisphysicochemical-properties+1
    Peptide cutter

    Peptide cutter

    Map protease and chemical cleavage sites across protein sequences for proteomics experiment planning.

    protein-analysisphysicochemical-properties+2
    CleaveNet

    CleaveNet

    Predict MMP cleavage z-scores, evaluate substrates, and generate conditional peptides.

    protein-analysisai-powered+4
    Protein parameters

    Protein parameters

    Calculate molecular weight, pI, extinction coefficients, composition, and sequence indices.

    protein-analysisphysicochemical-properties+1
  3. Immunogenicity and developability review

    Compare immune-response risk, solubility, and stability signals before structural follow-up.

    DeepImmuno

    DeepImmuno

    Score, compare, and generate peptide candidates with the official DeepImmuno models.

    protein-analysisdeep-learning+3
    TLimmuno2

    TLimmuno2

    Transfer learning-based MHC-II immunogenicity prediction for CD4+ T cell epitopes

    protein-analysisdeep-learning+3
    NetSolP-1.0

    NetSolP-1.0

    Predict protein solubility and purification usability for E. coli expression systems

    protein-analysisproperty-prediction+3
    Protein stability prediction

    Protein stability prediction

    Compare independently interpretable sequence properties related to protein stability.

    protein-analysisphysicochemical-properties+2
  4. Structure and binding review

    Model shortlisted peptides, validate geometry, and dock them against the target to explore compatible peptide–target complexes.

    HighFold

    HighFold

    Cyclic peptide structure prediction with CycPOEM-enhanced AlphaFold2

    protein-foldingstructure-prediction+3
    ESMfold

    ESMfold

    Predict protein structures and multimers directly from sequences without an MSA.

    protein-foldingstructure-prediction+2
    Boltz-2

    Boltz-2

    Predict biomolecular complex structures and binding affinities for proteins, ligands, DNA, and RNA.

    protein-foldingstructure-prediction+5
    RAPiDock

    RAPiDock

    All-atom protein-peptide docking with unranked samples.

    protein-dockingprotein+3
    LightDock

    LightDock

    Protein-protein, protein-peptide, and protein-DNA docking using Glowworm Swarm Optimization

    protein-dockinginteraction-prediction+4
    MolProbity

    MolProbity

    Validate protein structures with clashscore, Ramachandran, rotamer, and geometry checks.

    structure-analysisquality-validation+4

Frequently asked questions

ProteinIQ helps keep those signals together before laboratory testing. You can design or import peptides, calculate sequence properties, screen activity-related predictions, model structures, and compare the resulting tables and files without losing the relationship to each candidate. Start with a peptide sequence, a target, or a candidate library and run the checks needed for your decision. ProteinIQ returns the method-specific scores, structures, logs, and exports so a shortlist can be reviewed with its supporting evidence intact.

ProteinIQ supports peptide discovery workflows for sequence design, peptide property calculation, cleavage analysis, activity prediction, solubility review, immunogenicity-style triage, and structure follow-up. You can use these workflows to move from candidate sequences to reviewable computational evidence without writing local scripts.

ProteinIQ peptide tools commonly start from raw peptide sequences or FASTA records. Structure follow-up tools may require protein-style FASTA inputs or existing structure files, and each ProteinIQ workflow keeps those input requirements tied to the upstream tool being run.

Yes. ProteinIQ can run peptide design tools that generate candidate sequences, then route those candidates into property, activity, solubility, cleavage, and structure checks. The generated peptides should be treated as computational candidates for prioritization, not as experimentally validated hits.

ProteinIQ can help review peptide activity and liability signals such as antimicrobial or functional activity predictions, cleavage behavior, sequence properties, and developability-related descriptors when supported by the selected tool. The platform keeps the prediction labels and score tables visible so researchers can compare candidates directly.

ProteinIQ peptide property tools can calculate descriptors such as mass, charge, composition, cleavage products, hydropathy, and related sequence features depending on the tool. These calculations are presented as inspectable tables and downloads so the peptide sequence remains connected to the property evidence.

Yes. ProteinIQ can route peptide or short protein sequences into compatible structure prediction and modeling tools when the upstream method supports the input. Structure outputs can include PDB or CIF files, confidence information, logs, and other artifacts for downstream review.

Yes. ProteinIQ peptide workflows are useful when you want connected design, property, activity, and structure checks, but individual tools such as peptide mass, peptide cleavage, activity prediction, and folding tools can also be opened directly for a narrower question.

Yes. ProteinIQ peptide workflows can export FASTA sequences, generated candidate lists, CSV property tables, activity prediction tables, structure files, logs, and upstream result artifacts depending on the tool. Exports are intended to keep the computational evidence available for review outside ProteinIQ.

No. ProteinIQ provides computational peptide discovery and prioritization evidence. Experimental activity, toxicity, stability, permeability, immunogenicity, and developability assays are still required before making biological, therapeutic, or product claims about a peptide candidate.

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ProteinIQ

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