In Silico Design
3D Structural Modeling
5+ Prediction Algorithms
≥85% Humanization
1–2 Week Turnaround
Service Overview
Therapeutic antibodies derived from non-human species — most commonly rodents — carry immunogenic framework regions that can trigger anti-drug antibody (ADA) responses in patients, limiting efficacy and tolerability. Humanization replaces non-human framework residues with their human germline counterparts while preserving the antigen-binding complementarity-determining regions (CDRs), yielding a molecule that is immunologically indistinguishable from a fully human antibody at the framework level. Traditional CDR grafting approaches often sacrifice binding affinity or introduce manufacturability liabilities in the process. ICDMO's in silico humanization platform addresses this challenge by integrating three-dimensional structural analysis, multi-parameter immunogenicity prediction, and physics-based free-energy calculations to design humanized antibodies that simultaneously optimize humanness, binding potency, biophysical stability, and production fitness — before a single experiment is run. Our computational workflow is grounded in rigorous structural biology and supported by a validated set of bioinformatics tools for epitope mapping, surface characterization, and post-translational modification (PTM) risk assessment. Each design deliverable includes a comprehensive analysis report and a ranked set of humanized sequence variants ready for gene synthesis and expression testing.
Key Features & Advantages
Humanization Percentage
Framework humanness maximized to ≥85% (Kabat/IMGT) while preserving CDR loop conformation and canonical geometry.
CDR Immunogenicity
T cell, B cell, and MHC II epitope burden within CDR loops minimized using five validated prediction algorithms in parallel.
Antigen Binding Affinity
Binding affinity retention constrained to ≥50% vs. parental antibody by MM-GBSA free-energy estimation on the Fv–antigen complex.
Expression & Manufacturability
Manufacturability flags (aggregation-prone regions, unpaired cysteines, rare codons) resolved to support robust CHO/HEK expression.
Aggregation Potential
Hydrophobic and aggregation-prone surface patches identified and eliminated or minimized to improve formulation stability.
Thermodynamic Stability
Thermodynamic stability (Tm) and long-term colloidal stability maintained or improved relative to the parental antibody.
Sequence Integrity (PTM)
Deamidation, oxidation, glycosylation and proteolysis liability sites mapped and de-risked throughout framework and CDRs.
Bioinformatics Analysis Suite
1PTM analysis — deamidation, oxidation, glycosylation, and proteolysis motif mapping onto 3D model
2Aggregation surface analysis — identification and scoring of hydrophobic surface clusters
3Electrostatic patch analysis — positive, negative, and hydrophobic patch characterization
4T cell epitope prediction using AMPHI and Rothbard–Taylor algorithms
5B cell epitope prediction across the antigen surface, reported with per-residue confidence
6MHC II epitope prediction using Sette algorithm
7Antigenicity scoring using Jameson–Wolf and Welling methods
8Humanization percentage calculation (Kabat / IMGT definitions)
Back-Mutation Decision Framework
Structural Integrity Criterion
▸Substitution disrupts an ionic bond, hydrogen bond, or hydrophobic interaction with a CDR residue
▸Substitution affects a canonical residue, VH/VL interface residue, or Vernier zone residue
▸Substitution introduces steric clash or alters CDR canonical loop geometry
Biophysical Liability Criterion
▸Substitution measurably increases predicted immunogenicity epitope burden
▸Substitution increases aggregation-prone surface area or positive patch intensity
▸Substitution introduces a new 3D PTM motif (deamidation, oxidation, glycosylation site)
▸Substitution causes significant shift in 3D isoelectric point (pI)
ICDMO Quality Standards
Standard 1 — Humanization ≥85%
▸The proportion of human germline residues in combined VH/VL framework regions must reach ≥85% by Kabat/IMGT definition
▸This level of humanness is associated with substantially reduced anti-drug antibody (ADA) risk in clinical use
▸All delivered variants are scored and reported against this threshold before recommendation
Standard 2 — Binding Retention ≥50% vs. Parental
▸Predicted binding free energy of the humanized design must not exceed a 2-fold reduction vs. parental antibody
▸Computationally assessed by MM-GBSA free-energy estimation on the ternary Fv–antigen complex
▸Subsequently confirmed by wet-lab SPR or BLI experiments on expressed humanized variants
Deliverables
1Ranked humanized VH/VL sequence variants in FASTA format
2Comprehensive 3D structural analysis report with annotated Fv models
3Immunogenicity epitope comparison — parental vs. humanized (all algorithms)
4Surface patch and aggregation risk assessment with visual maps
5PTM liability mapping for each proposed variant
6Detailed back-mutation rationale document with structural justification
What We Need From You
1Parental VH and VL sequences with the species of origin stated
2Antigen information and any structural or epitope mapping data available
3Measured affinity, stability and expression data for the parental antibody, used as the benchmark
4The intended clinical context, which determines how much immunogenicity risk is acceptable
5How many variants you can express and characterise, which sets the size of the designed series
How the Work Is Performed
1Germline assignment, CDR definition and identification of the structurally critical framework positions
2Structural modelling of the parental variable domains, with the antigen complex where available
3Human framework selection balancing sequence identity, canonical class compatibility and germline frequency
4CDR grafting with structural evaluation of the graft junctions and the loops that support them
5Back-mutation design informed by Vernier zone, interface and canonical structure analysis
6Humanness scoring, MHC class II epitope prediction and developability liability screening
What You Receive
1Graded series of humanised sequences from conservative through to fully germline-matched
2Humanness scores and predicted immunogenicity assessment for every variant
3Structural models showing the graft and the rationale for each proposed back-mutation
4Developability liability report covering the designed sequences
5Recommended expression and testing order across the series
Interpretation and Limitations
Humanness scores and MHC class II predictions indicate relative immunogenicity risk; they do not predict clinical anti-drug antibody responses, which also depend on aggregation, dose, route and patient population. Affinity retention after grafting cannot be predicted reliably, which is why a graded series is delivered for measurement. Expression and binding characterisation are performed by your team or a partner.
Questions We Are Asked Before Scoping
How much affinity will we lose?
▸It varies and cannot be predicted reliably. Delivering a graded series lets a small expression panel establish where affinity is lost, which is faster and cheaper than iterating on single constructs.
Is a high humanness score enough?
▸It correlates with lower immunogenicity risk but does not guarantee it. We report both germline content and predicted T-cell epitope content, since they capture different aspects of the risk.
Can you humanise a nanobody?
▸Yes, with particular attention to the camelid framework-2 hallmark residues that govern solubility in the absence of a light chain. Those positions are treated explicitly rather than germlined by default.
Service Workflow
1
3D Antibody Modeling
Build a high-accuracy homology model of the parental antibody Fv/Fab domain from VH/VL sequence input. Identify CDR loops, canonical residue positions, and CDR–antigen contact residues that must be protected during CDR grafting.
2
Immunogenicity Epitope Analysis
Predict T cell, B cell, and MHC II immunogenic epitopes on both the parental sequence and the 3D structural surface using five validated bioinformatics algorithms (AMPHI, Rothbard–Taylor, DNASTAR, Sette, Jameson–Wolf).
3
Surface & PTM Liability Analysis
Characterize positive, negative, and hydrophobic electrostatic patches. Score aggregation-prone surface regions. Map all PTM liability sites (deamidation, oxidation, glycosylation, proteolysis) with side-chain accessibility scoring.
4
Human Germline Acceptor Selection
BLAST search IMGT and NCBI germline databases to identify VH and VL germline genes with highest sequence identity to the parental framework. Assess 3D structural compatibility to ensure selected acceptor accommodates parental CDR conformations.
5
CDR Grafting & Back-Mutation Design
Graft parental CDRs onto the selected human germline acceptor framework. Apply the back-mutation decision criteria to each non-human → human position. Deliver a ranked panel of optimized humanized variants satisfying both quality standards.
Service Process
1
Online Consultation
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2
Solution Matching
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3
Service Contract
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Project Execution
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5
Data Delivery
Specifications & Turnaround
Note: ICDMO delivers computational (in silico) services. Results prioritise hypotheses for testing; they do not by themselves establish binding, biological activity, efficacy or safety. All deliverables are for research use only and are not intended for diagnostic or therapeutic use. Downstream experimental work is scoped separately and executed through qualified partners.
Get a Custom Quote
Our scientific team responds within 24 hours with a detailed technical proposal and pricing tailored to your project.
Contact Us Online ConsultationStandard Deliverables
✓Sequence-verified final product
✓Full QC documentation
✓Certificate of Analysis (CoA)
✓Electronic data files
✓Project completion report
Why ICDMO?
Computational CDMO Focus
Reproducible, Versioned Pipelines
Confidence & Limitations Reported
Experiment-Aware Recommendations
Response Within One Business Day