Protective Antigens from Any Pathogen. Computationally Predicted, Experimentally Proven
Bring us your pathogen. We computationally mine its proteome for protective epitopes, validate them in challenge models, and deliver defined antigen candidates ready for vaccine development. Pathogen-agnostic. Species-agnostic.
Thousands of proteins. Which ones protect?
Discovering vaccine antigens by empirical screening is slow, expensive, and blind. A pathogen's proteome may encode thousands of open reading frames, but fewer than five typically confer protection. Finding them requires computational precision and experimental validation.
Empirical Antigen Discovery Is Slow and Blind
Whole-organism immunization followed by months of screening with no computational guidance, no structural insight, no rational prioritization. You test everything and hope something works.
Vast Proteomes, Vanishingly Few Protective Targets
Thousands of ORFs in a typical pathogen genome, but fewer than five induce protective immunity. Without systematic epitope prediction, you're looking for a needle in a haystack with no magnet.
Single-Strain Antigens Fail Against Variants
Antigens selected from a single reference strain break on antigenic drift. Without pan-genome analysis and cross-strain epitope conservation mapping, your vaccine may protect against the lab strain but not the field.
Epitope Definition Meets Immune Targeting
Our DIRECT platform integrates structural bioinformatics, pan-genome analysis, and iterative challenge validation into a single antigen discovery workflow, replacing empirical screening with defined, data-driven antigen selection.
Pathogen Proteome
Genome mining, ORF annotation, surface protein identification
We map every potential target in your pathogen
Epitope Definition
Structural modeling, B/T-cell prediction, conservation scoring
Computationally rank epitopes by protective potential
Immune Targeting
Immunization, challenge, correlate analysis, iterative refinement
Experimentally validate and refine until protection is proven
Structural bioinformatics identifies surface-exposed, conserved epitopes. Pan-genome analysis ensures cross-strain coverage. Challenge validation proves protection, not just immunogenicity.
Antigen Discovery Pipeline
A structured workflow from pathogen genome to validated lead antigens. Each node is a specific scientific activity with defined techniques and deliverables. Branch nodes show parallel activities alongside the main pipeline.
Modular by Design. Pick What You Need
Need just proteome mining and epitope prediction? Just antigen expression? Just challenge studies with your existing candidates? Engage for any set of nodes, or the full end-to-end discovery program. We scope to your pathogen and your timeline.
Pathogen Genomics & Proteome Mining
We start with your pathogen's genome, or we sequence it. Open reading frame identification, functional annotation, subcellular localization prediction, and pan-genome analysis across available strains to identify the core proteome that defines your target.
Structural Bioinformatics & Epitope Prediction
For each candidate surface protein, we build structural models and predict B-cell epitopes, both linear and conformational. Surface accessibility scoring, disorder prediction, and variant mapping identify regions that are both immunogenic and conserved across strains.
T-Cell Epitope Prediction
For vaccine programs requiring cellular immunity, we predict MHC-I and MHC-II binding peptides with population coverage analysis across HLA supertypes. Critical for intracellular pathogens and cancer vaccine applications.
Candidate Antigen Panel Design
We integrate B-cell and T-cell epitope data with structural and conservation analyses to design a multi-epitope antigen panel. Typically 8–15 candidates optimized for cross-strain coverage, surface accessibility, and expression feasibility.
Recombinant Antigen Expression
We express your antigen panel recombinantly: codon-optimized, gene-synthesized, and produced in the expression system best suited to each construct. Purification to immunization-grade quality with full characterization.
Immunization & Challenge Studies
We design and execute immunization protocols with your antigen panel: adjuvant selection, prime-boost scheduling, and comprehensive immune response profiling. For programs with challenge models, we validate protection directly.
Immune Correlate Analysis
We analyze immune responses across protective and non-protective groups to identify correlates of protection: antibody titers, T-cell responses, mucosal IgA, and functional assay readouts that predict vaccine efficacy.
Iterative Refinement
Based on challenge results, we cycle back, comparing protective vs. non-protective antigens, updating computational predictions, and refining the candidate panel. This feedback loop is what separates defined antigen discovery from empirical screening.
Lead Antigen Validation & Delivery Matching
Final lead antigens undergo powered challenge studies with statistical rigor, cross-strain validation against divergent isolates, and matching to the optimal delivery modality: saRNA, probiotic, DNA, or subunit formulation.
Timeline Overview
Computational candidates in weeks, not months. Our pipeline delivers actionable results at every milestone.
Proteome Mining
Genomics, annotation, structural modeling
Wk 1–4Epitope Prediction
Computational analysis & panel design
Wk 3–8Antigen Expression
Recombinant production & QC
Wk 6–14Immunization & Challenge
Animal studies & protection data
Wk 12–28Refinement & Validation
Iterative improvement & lead confirmation
Wk 26–36+Computational candidates in 8 weeks, first challenge data by Week 28, full program with iterative refinement in 36 weeks.
Technical Capabilities
End-to-end vaccine antigen discovery infrastructure, from genome to validated antigen.
Structural Bioinformatics
AlphaFold2 and homology modeling for structure prediction. Disorder analysis, solvent-accessible surface area mapping, and B-cell epitope scoring from 3D structures.
Epitope Prediction Algorithms
BepiPred for linear B-cell epitopes, DiscoTope for conformational epitopes, NetMHCpan for T-cell binding, plus custom scoring integrating conservation and accessibility.
Recombinant Antigen Expression
E. coli, baculovirus/Sf9, and HEK293 expression systems. Codon optimization, gene synthesis, affinity purification, and SEC polishing to immunization-grade quality.
Challenge Model Development
Animal model selection, clinical endpoint design, statistical powering for challenge studies. We validate protection, not just immunogenicity.
Immune Response Profiling
ELISA (total IgG, subclass, endpoint titer), ELISpot, flow cytometry for T-cell responses, and mucosal IgA quantification. Full humoral and cellular immune readouts.
Pan-Genome & Variant Analysis
Core vs. accessory genome classification, epitope conservation scoring across strains, antigenic drift tracking, and cross-strain coverage optimization.
Delivery Platforms
Once we define your lead antigens, we match them to the optimal delivery modality. The platform choice is biology-driven: pathogen, route, and immune response profile determine the best fit.
Self-Amplifying RNA (saRNA)
LNP-formulated self-amplifying RNA. Strong humoral and cellular immune responses with lower dose requirements than conventional mRNA.
Recombinant Probiotic
Oral delivery via engineered probiotic strains. Mucosal immunity induction, no cold chain requirement, and natural adjuvant effects.
DNA Vaccine
Plasmid-based DNA vaccines. Thermostable, scalable manufacturing, and strong T-cell responses. Suitable for resource-limited settings.
Algal Expression
Microalgae-based antigen expression. GRAS organism, edible vaccine potential, low-cost production for global health applications.
Delivery Selection Is Biology-Driven
We recommend delivery platform selection as part of every antigen discovery program. The right modality depends on your pathogen, target species, desired immune response profile, and deployment context. We help you match biology to platform.
IP & Engagement Model
Your pathogen, your antigens, your vaccine. Our platform stays ours, available for your next pathogen program.
What You Own
Your pathogen, your antigens. Full IP rights to discovered candidates
- All antigen sequences, expression constructs, and structural models
- Challenge data, immune response profiles, and correlate analyses
- Delivery-matched antigen formulations and manufacturing protocols
- Freedom to develop, license, partner, or manufacture independently
Our Platform
Proprietary infrastructure powering reproducible antigen discovery
- Epitope prediction algorithms and custom scoring models
- Pan-genome analysis pipelines and variant tracking databases
- Challenge model protocols and statistical analysis frameworks
- Iterative refinement methodology and feedback loop architecture
Flexible Engagement Models
Fee-for-service, milestone-based, or co-development partnerships. We structure the engagement to match your pathogen, your pipeline stage, and your development timeline.
Integrated Services
Your vaccine antigen program connects directly to the broader NexysBio platform. Same team, same context, zero transfer delays.
Nano-Drug Formulation
LNP and polymer nanoparticle formulation for antigen delivery, including saRNA encapsulation, subunit adjuvant formulations, and controlled-release antigen depots.
View serviceAntibody Engineering
Generate monoclonal antibodies against your discovered antigens for diagnostic, therapeutic, or correlate-of-protection applications.
View serviceBiomarker Discovery
Multi-omics immune biomarker profiling: host response signatures and correlates of protection feeding directly into vaccine development programs.
View serviceEnzyme & Protein Engineering
Engineered antigens with improved immunogenicity and stability. Recombinant production across E. coli, Pichia, insect, and mammalian systems.
View serviceBio-Digital Solutions
Custom software built by scientists who understand your workflows, from data dashboards to regulatory-compliant systems.
View serviceCell-Based Assay Services
Functional immune assays, neutralization testing, and cell-based readouts integrated directly into your vaccine discovery program.
Have a pathogen that needs a vaccine?
Let's design your antigen discovery program, from proteome mining through challenge validation. We'll scope the right combination of computational and experimental nodes for your pathogen and timeline.
Or email us directly at info@nexysbio.com