Peptide discovery workflows
Discover peptides builtfor binding and activity.
Design, screen, and characterize peptide candidates across sequence properties, activity signals, structure predictions, and developability checks before experimental follow-up.
Result generated with Boltz-2
Capabilities
Peptide discovery models
PepMLM
Design linear peptide binders for target proteins using a target sequence-conditioned masked language model. PepMLM generates peptide sequences optimized to bind specific protein targets based on ESM-2 protein language modeling.
BoltzGen
BoltzGen is a state-of-the-art AI model for designing protein and peptide binders against any biomolecular target. Using generative diffusion models, it creates novel binders (proteins, peptides, nanobodies) with nanomolar-level binding affinity.
TLimmuno2
Predict MHC class II peptide immunogenicity (CD4+ T cell response) using transfer learning with LSTM.
CleaveNet
Official CleaveNet tool for matrix metalloproteinase cleavage prediction and peptide generation. Predict cleavage z-scores plus uncertainty across 17 MMP variants, evaluate against truth z-scores, or generate candidate peptides unconditionally or from MMP z-score profiles.
Peptide cutter
Predict protease and chemical cleavage sites across a protein sequence for up to 39 enzymes simultaneously. Identify where each enzyme cuts, the cleavage residue, and context window around each site.
Boltz-2
Boltz-2 is a biomolecular foundation model for structure and binding affinity prediction. Supports proteins, ligands, DNA, and RNA in multi-component complexes. Automatically scales GPU resources for large complexes. Predicts binding affinity with near-FEP accuracy at 1000x faster speed.
Read to research?
Free
Includes:
- 100 credits
- 3 jobs per day
- 1 concurrent job
- 1 workflow
- 1 seat
- Core tool features
- Academic license
Lite
Everything Free, plus:
- 500 credits / month
- No daily job limit
- 2 concurrent jobs
- 3 workflows
- Advanced tool settings
- AI assistant, SVG export, batch runs, and workflows
Plus
Everything Lite, plus:
- 2,000 credits / month
- 5 concurrent jobs
- 5 workflows
Pro
Best valueEverything Plus, plus:
- 8,000 credits / month
- 10 concurrent jobs
- 20 workflows
- Commercial license
Questions & answers
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.