Antibody Engineering Service

From Target to Therapeutic Antibody. Conventional Meets Computational

Two parallel pipelines, conventional hybridoma discovery and our proprietary in-silico evolution platform, converge to deliver antibodies that are faster to develop, higher in affinity, and validated by both wet-lab and computational methods.

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You have a promising target. Who builds the antibody?

Generating a high-quality therapeutic antibody against your target requires immunization infrastructure, display platform expertise, computational design capabilities, and functional validation, rarely found under one roof.

Conventional Methods Are Slow & Unpredictable

Hybridoma campaigns take months with no guarantee of success. You may generate hundreds of clones and still lack a lead with the affinity, specificity, and developability profile you need.

Purely Computational Lacks Wet-Lab Validation

In-silico designs look great on paper but fail in practice. Without rapid wet-lab validation cycles, computational predictions remain theoretical, and your program stalls at the first expression bottleneck.

No Single Provider Bridges Both Worlds

You end up stitching together a computational CRO, a hybridoma shop, a display platform vendor, and an expression house. Context is lost at every handoff. Timelines balloon. Candidates fall through the cracks.

Two Pipelines, One Platform

We run conventional antibody discovery and computational antibody evolution in parallel, and bridge them with cross-platform intelligence transfer. The result: better antibodies, faster.

Conventional Discovery

Immunization, hybridoma, yeast display: proven wet-lab methods

Generates real binders from immune repertoires

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Cross-Platform Intelligence

Data flows between pipelines. Each makes the other better

ML learns from wet-lab; computation guides screening

In-Silico Evolution

ML-driven design, virtual screening, CDR optimization

Explores sequence space no animal can reach

Our proprietary platform enables wet-lab validated, computationally optimized antibodies, with cross-platform intelligence making each pipeline stronger than either alone.

Dual Service Pipeline

Two parallel pipelines with cross-platform bridges. Each node is a specific scientific activity. Engage for any combination, or the full dual-pipeline program.

Modular by Design. Pick What You Need

Run conventional discovery alone. Run in-silico evolution alone. Run both in parallel with cross-platform intelligence. Or engage for specific nodes: hybridoma sequencing, yeast display panning, computational IgG reconstruction. We scope to your program.

Conventional Discovery

Wet-lab antibody generation through immunization, hybridoma, and display platforms

Target Antigen Preparation

Recombinant expression of the target antigen in appropriate host systems (E. coli, HEK293, baculovirus). Purification, quality control, and characterization to ensure correct folding and epitope presentation.

Methods

Recombinant expression (prokaryotic & eukaryotic)Affinity & size-exclusion chromatographySDS-PAGE, Western blot, SEC-MALS validation

Deliverables

Purified antigen (mg-scale)QC characterization report

Animal Immunization

Antigen formulated with optimized adjuvant system. Multi-dose boost schedule with titer monitoring at each timepoint. Serum collected and characterized for antigen-specific IgG response.

Methods

Adjuvant optimization & formulationPrime-boost immunization scheduleSerum titer monitoring (ELISA)Terminal bleed & splenocyte harvest

Deliverables

Immune serum with confirmed titersSplenocytes for fusion

Hybridoma Generation

Splenocyte-myeloma fusion using optimized PEG or electrofusion protocols. HAT selection, limiting dilution cloning, and initial screening against target antigen to identify positive clones.

Methods

PEG / electrofusion protocolsHAT medium selectionLimiting dilution cloningPrimary ELISA screening

Deliverables

Positive hybridoma clonesInitial binding data

Hybridoma Sequencing & Deconvolution

All positive hybridomas are sequenced to obtain variable region (VH/VL) sequences. Germline gene usage, CDR3 diversity, and somatic hypermutation patterns are assessed. Minimal biofunctional antibody candidates identified based on sequence features.

Methods

V-region RT-PCR & Sanger sequencingGermline gene assignment (IMGT)CDR3 length & diversity analysisSomatic hypermutation profiling

Deliverables

Full VH/VL sequencesGermline analysis reportCandidate shortlist

Yeast Surface Display Panning

Antibody variable regions reformatted as scFv or Fab fragments and displayed on yeast surface. Multiple rounds of FACS-based selection against recombinant antigen and epitope peptides to enrich high-affinity binders.

Methods

scFv/Fab yeast display library constructionFACS-based selection roundsEnrichment tracking (input/output ratios)Counter-selection against off-targets

Deliverables

Enriched binder poolRound-over-round enrichment data

Functional Screening

Enriched candidates screened by ELISA against full-length recombinant antigen, epitope peptides, and minimal domain constructs. Binding specificity, cross-reactivity, and epitope bin assignment determined.

Methods

ELISA: recombinant antigenELISA: epitope peptide panelsELISA: minimal domain constructsEpitope binning (competitive ELISA)

Deliverables

Binding profiles per candidateEpitope bin assignmentsLead panel selection

Lead Selection & Expression

Top candidates selected based on binding, specificity, and sequence liabilities. Leads reformatted to full IgG, expressed in Pichia pastoris or CHO cells, and purified for downstream characterization.

Methods

Clone sequencing & liability assessmentIgG reformatting & codon optimizationPichia / CHO transient expressionProtein A / affinity purification

Deliverables

Purified IgG leads (mg-scale)Expression yield dataPurity assessment (SEC, SDS-PAGE)

Data Transfer

Conventional hybridoma and panning data feeds into the in-silico platform — ML models learn from wet-lab results to generate enhanced candidates with higher predicted Kd.

Data Transfer

Epitope Guidance

In-silico predicted epitopes and minimal domain architecture guide the design of screening antigens used in the conventional pipeline — more focused assays, less noise.

Epitope Guidance

Shared Validation

Yeast surface display results from both pipelines are cross-validated — the best candidates advance regardless of origin, with full sequence and binding data shared between platforms.

Shared Validation

In-Silico Evolution

ML-driven antibody design, virtual screening, and computational optimization

Target Epitope Computation

Computational prediction of immunodominant and functional epitopes on the target antigen. Structure-based analysis to identify surface-exposed, conserved regions. Design of minimal domain architecture for focused antibody generation.

Methods

Structure-based epitope predictionConservation & surface accessibility analysisMinimal domain architecture designB-cell epitope scoring algorithms

Deliverables

Predicted epitope mapMinimal domain constructs designedTarget epitope ranking

In-Silico Antibody Library Generation

Machine learning-driven generation of antibody variable region sequences. Massive permutation space reduced computationally to focus on sequences with high predicted binding probability to target epitopes.

Methods

ML-driven sequence generationPermutation space reduction algorithmsEpitope-targeted library designSequence diversity & coverage optimization

Deliverables

Focused virtual library (10³–10⁴ sequences)Diversity metrics report

CDR-Focused Diversity Design

Specific CDR positions selected computationally for diversification. Framework regions kept minimal to preserve stability. CDR-H3 loop modeling guides length and composition choices for optimal target engagement.

Methods

Position-specific CDR diversificationCDR-H3 loop length optimizationFramework stability preservationStructural modeling of CDR conformations

Deliverables

CDR-focused library designPosition-specific diversity maps

Virtual Screening & Ranking

Computational screening of the virtual library against target epitopes. Binding affinity prediction, structural stability scoring, and developability filters (aggregation propensity, viscosity, immunogenicity risk) applied to rank candidates.

Methods

Binding affinity prediction (docking/ML)Structural stability scoringAggregation propensity predictionImmunogenicity risk assessment

Deliverables

Ranked candidate listPredicted Kd valuesDevelopability scorecards

Yeast Surface Display Validation

Top computationally predicted candidates expressed on yeast surface. Panning against recombinant antigen and epitope peptides validates in-silico predictions and identifies true binders with confirmed affinity.

Methods

Synthetic gene library constructionYeast surface display expressionFACS panning: recombinant antigenFACS panning: epitope peptides

Deliverables

Validated binder setPredicted vs. actual binding correlation

Functional Screening

Validated candidates screened by ELISA against recombinant antigen, epitope peptides, and minimal domain architecture constructs. Cross-platform comparison with conventional pipeline candidates where applicable.

Methods

ELISA: recombinant antigenELISA: epitope peptide panelsELISA: minimal domain architectureCross-platform candidate comparison

Deliverables

Binding profilesCross-platform performance dataFunctional lead panel

Computational IgG Reconstruction

ScFv or nanobody leads stitched back into full IgG framework with isotype-specific constant regions. Molecular dynamics folding analysis validates structural integrity. Antigenicity prediction and glycosylation pattern analysis ensure developability.

Methods

IgG framework reconstruction (isotype-specific)Molecular dynamics folding simulationAntigenicity prediction algorithmsGlycosylation pattern analysis

Deliverables

Reconstructed IgG sequencesMD folding validation reportDevelopability assessment

Expression & Characterization

Computationally optimized IgG leads expressed in Pichia pastoris or CHO cells. Purified antibodies characterized for binding kinetics (SPR/BLI), thermal stability, and aggregation propensity.

Methods

Pichia / CHO expressionProtein A / affinity purificationSPR / BLI binding kineticsThermal stability (DSF/DSC)

Deliverables

Purified IgG leadsKinetic data (kon, koff, Kd)Stability & developability profile

Cross-Platform Bridges

Data TransferConventional → In-Silico

Conventional hybridoma and panning data feeds into the in-silico platform — ML models learn from wet-lab results to generate enhanced candidates with higher predicted Kd.

Epitope GuidanceIn-Silico → Conventional

In-silico predicted epitopes and minimal domain architecture guide the design of screening antigens used in the conventional pipeline — more focused assays, less noise.

Shared ValidationBidirectional

Yeast surface display results from both pipelines are cross-validated — the best candidates advance regardless of origin, with full sequence and binding data shared between platforms.

Timeline Overview

Two pipelines running in parallel. The in-silico track delivers characterized leads by Week 30 while conventional discovery runs to Week 45. Cross-platform bridges keep both pipelines informed throughout.

Conventional

~45 weeks

Ag Prep

Immunization

Hybridoma & Seq

Display & Screen

Lead Expression

In-Silico

~30 weeks

Computation & Design

Yeast Validation

Screen & Recon

Express & Char

In-Silico leads ready, Week 30

Conventional leads ready, Week 45

Wk 3: Epitope data transfer

Wk 20: Cross-validation bridge

Weeks from program start

Conventional Pipeline~45 weeks

Antigen PrepWk 1–5

ImmunizationWk 5–21

Hybridoma & SequencingWk 21–30

Display & ScreeningWk 30–39

Lead ExpressionWk 39–45

In-Silico Pipeline~30 weeks

Computation & DesignWk 1–10

Yeast ValidationWk 10–18

Screening & ReconstructionWk 18–24

Expression & CharacterizationWk 24–30

In-silico pipeline delivers characterized antibody leads by Week 30. Conventional pipeline delivers by Week 45. Running both in parallel with cross-platform intelligence gives you the best candidates from both worlds, typically a cross-validated lead panel by Week 33–36.

Technical Capabilities

Integrated antibody engineering infrastructure, from computation to characterization.

Yeast Surface Display Platform

High-throughput scFv/Fab display on yeast surface with FACS-based multi-round panning. Enables affinity maturation and selection against recombinant antigens, epitope peptides, and whole cells.

Computational Epitope Mapping

Structure-based epitope prediction using surface accessibility, conservation analysis, and B-cell epitope scoring. Designs minimal domain architectures for focused antibody generation campaigns.

Hybridoma Development & Sequencing

Full hybridoma generation pipeline from immunization through fusion, cloning, and V-region sequencing. Germline analysis and deconvolution identify optimal candidates for advancement.

Pichia & CHO Expression Systems

Recombinant antibody expression in both Pichia pastoris (cost-effective, rapid) and CHO cells (mammalian glycosylation). Protein A purification and SEC-based polishing for research and preclinical grade material.

Binding Kinetics & Affinity Analysis

SPR (Biacore) and BLI (Octet) kinetic measurements: kon, koff, and equilibrium Kd determination. Multi-concentration kinetic fits with full sensorgram analysis and affinity ranking across candidate panels.

Functional Assays (Neutralization, Reporter)

Virus neutralization assays (plaque reduction, pseudovirus), toxin neutralization, and cell-based reporter assays. Validated functional readouts beyond simple binding confirmation.

Functional Assay Platform

Beyond binding, we validate that your antibodies work. Neutralization, reporter, and custom functional assays built into the same pipeline.

Virus Neutralization Assays

Plaque reduction neutralization tests (PRNT) and pseudovirus neutralization assays for enveloped and non-enveloped viruses. Dose-response curves with IC50/IC90 determination.

PRNTPseudovirusIC50/IC90

Toxin Neutralization

Cell-based toxin neutralization assays measuring antibody-mediated protection. Quantitative dose-response with comparison to reference antibodies where available.

Cell protectionDose-responseReference comparison

Cell-Based Reporter Assays

Engineered reporter cell lines for pathway-specific readouts: receptor blocking, signaling inhibition, and ADCC reporter assays. Cross-link to our nano-formulation platform for custom reporter development.

Reporter cellsADCCSignaling

We build the reporters you need

Biofunctional Assays

Custom biofunctional assays designed to client specifications: complement activation, Fc receptor binding, internalization kinetics, and application-specific readouts.

Custom designFc functionInternalization

IP & Engagement Model

Your target, your antibody, your IP. Our platform stays ours, available for your next program or licensed for internal use.

What You Own

Your target, your antibody. Full IP rights to your engineered leads

All antibody sequences (VH/VL, full IgG) and variants generated
Binding kinetics data (SPR/BLI), affinity measurements
Functional assay results (neutralization, reporter, custom)
Expression constructs, cell lines, and purification protocols
Freedom to manufacture, license, or partner with no reach-back

Our Platform

Proprietary infrastructure powering reproducible antibody discovery

ML models for antibody library generation and virtual screening
Proprietary yeast surface display library construction protocols
Computational epitope mapping and CDR diversity design algorithms
IgG reconstruction and MD folding validation pipelines
Available for licensing or continued partnership engagements

Flexible Engagement Models

Fee-for-service, milestone-based, or co-development partnerships. We structure the engagement to match your program stage, risk profile, and development timeline.

Integrated Services

Your antibody program connects directly to the broader NexysBio platform. Same team, same context, zero transfer delays.

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Nano-Drug Formulation

Antibody-nanoparticle conjugation. Load your engineered antibody onto our polymer nanoparticle platform for targeted delivery. Same team, seamless handoff.

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Antibody-nanoparticle conjugation bridge

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Vaccine Antigen Discovery

Computationally mine pathogen proteomes for protective epitopes. Our antibody engineering platform feeds directly into antigen validation and challenge studies.

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Biomarker Discovery

Multi-omics biomarker discovery. Generate monoclonal antibodies against discovered protein biomarkers for ELISA development and diagnostic applications.

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Enzyme & Protein Engineering

Shared ML infrastructure and protein expression platforms. Engineered binding domains, enzyme-antibody fusions, and optimized antigen production.

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Bio-Digital Solutions

Custom software built by scientists who understand your workflows, from data dashboards to regulatory-compliant systems.

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Coming Soon

Cell-Based Assay Services

Functional validation of your antibodies in cell-based systems: neutralization, reporter, and custom assays using the same platform as our screening pipeline.

Have a target that needs an antibody?

Let's design your antibody engineering program: conventional, computational, or both. We'll scope the right combination of pipelines for your target and timeline.

Or email us directly at info@nexysbio.com