AIXC BioSciences Platform Antibody Docking
Antibody Engineering

IgFoldAI Prediction + HADDOCK3Docking Engine.
31/31 Tests Passing.

Complete antibody docking pipeline from sequence to CAPRI-quality complex structures. GPU-accelerated structure prediction, automated paratope detection, and restraint-driven docking.

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PIPELINE

Four-Stage Antibody Pipeline

From antibody sequence to docked complex with quality assessment. Each stage is automated and validated with production test suites.

Structure Prediction
IgFoldAI Engine
GPU-accelerated antibody structure prediction from VH/VL sequences. Fast and accurate CDR loop modeling.
Paratope Detection
ProABC-2
Identify binding residues on the antibody surface. Predict CDR loop involvement and framework contributions.
Antibody Docking
HADDOCK3Docking Engine
Information-driven docking using CDR restraints from paratope detection. Explicit solvent refinement for accurate interfaces.
Quality Assessment
CAPRI Metrics
Standardized CAPRI quality scoring: interface RMSD, ligand RMSD, fraction of native contacts. Ranked by DockQ score.
CORE TOOLS

Production-Grade Components

Each tool in the pipeline has been individually validated and integrated into a seamless automated workflow.

IgFoldAI Structure Prediction

Deep learning antibody structure prediction trained on the Observed Antibody Space database. Runs on GPU for fast inference.

GPU inference
Accurate CDR-H3 loop prediction
VH/VL pairing from separate sequences
Renumbered output (IMGT/Chothia/Kabat)

HADDOCK3Advanced Antibody Docking

Information-driven docking using CDR restraints from ProABC-2. Three-stage protocol: rigid-body, semi-flexible, and explicit solvent refinement.

CDR-derived ambiguous interaction restraints
Explicit water refinement stage
Clustering-based model selection
HADDOCKDocking score energy ranking
SUPPORTED FORMATS

Three Antibody Formats

Our pipeline handles the major therapeutic antibody formats, from single-chain variable fragments to full-length immunoglobulins.

scFv
Single-Chain Variable Fragment
VH-linker-VL single chain. Smallest functional binding unit. Ideal for CAR-T, bispecifics, and targeted delivery.
Fab
Fragment Antigen-Binding
VH-CH1 + VL-CL heterodimer. Full antigen-binding arm with constant domain stabilization. Used in ranibizumab, certolizumab.
Full IgG
Complete Immunoglobulin G
Full Y-shaped antibody with Fc region. Bivalent binding, Fc effector functions. Standard format for most therapeutic antibodies.

Full Test Suite Passing

All 31 integration tests pass across the complete antibody docking pipeline. Covers IgFoldAI prediction, ProABC-2 paratope detection, HADDOCK3restraint-driven docking, and CAPRI quality assessment. Continuous integration ensures no regressions.

31/31
Tests Passing
QUALITY STANDARDS

CAPRI Quality Assessment

Docking results are evaluated using the standard CAPRI (Critical Assessment of PRedicted Interactions) quality metrics.

Incorrect
fnat < 0.1
OR L-RMSD > 10 A
Acceptable
fnat ≥ 0.1
AND L-RMSD ≤ 10 A
Medium
fnat ≥ 0.3
AND (L-RMSD ≤ 5 A OR i-RMSD ≤ 2 A)
High
fnat ≥ 0.5
AND (L-RMSD ≤ 1 A OR i-RMSD ≤ 1 A)
GET STARTED

Ready for Antibody Docking?

Submit your antibody VH/VL sequences and antigen structure. We will deliver predicted complex structures with CAPRI quality scores and binding interface analysis.

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