How to Use TNP (Therapeutic Nanobody Profiler) Online
Try TNP
Commercially Available Online Web Server
TNP: The Therapeutic Nanobody Profiler for Developability Design
TNP (Therapeutic Nanobody Profiler) is a pioneering open-source computational tool designed to characterize and predict the developability of nanobodies. Developed by the Oxford Protein Informatics Group (OPIG), TNP extends the proven principles of the Therapeutic Antibody Profiler (TAP) to the unique single-domain format of nanobodies.
By accounting for nanobody-specific structural features—such as the exposed framework 2 (FR2) region and diverse CDR3 conformations—TNP enables researchers to identify potential manufacturing, storage, and immunogenicity risks early in the design cycle.
Key Innovations: Tailored Nanobody Intelligence
TNP moves beyond conventional antibody modeling to account for the distinct biophysical properties of VHH domains.
Nanobody-Specific Metrics: Features six core descriptors including total CDR length, CDR3 length, and a novel CDR3 compactness measure.
Surface Property Mapping: Calculates patches of surface hydrophobicity and charge specifically across the CDR vicinity to predict aggregation and non-specific binding risks.
Clinical Benchmarking: Calibrates all metrics against the 36 currently available clinical-stage nanobody sequences to establish "safe" developability ranges.
Conformational Clustering: Identifies structural subtypes based on whether CDR3 loops are "kinked" (folded over the FR2) or "extended" (reaching away from the framework).
Hallmark Residue Analysis: Monitors the nanobody "tetrad"—conserved hallmark residues in FR2 that enhance solubility and stability.
Performance & Clinical Guidelines
TNP uses a traffic-light flagging system to alert designers when a candidate's properties deviate from those of successful clinical-stage therapeutics.
Metric | Clinical Range | Amber Flag (Top/Bot 5%) | Red Flag (Outside Clinical) |
Total CDR Length | 20–39 residues | 20–24 or 37–39 | <20 or >39 |
CDR3 Length | 5–23 residues | 5–8 or 21–23 | >23 |
CDR3 Compactness | 0.56–1.61 | 0.56–0.81 or 1.57–1.61 | <0.56 or >1.61 |
Surface Hydrophobicity | 73.4–155.5 | 73.4–79.6 or 126.8–155.5 | Outside 73–155 |
Positive Charge Patches | 0.00–1.18 | 0.39–1.18 | >1.18 |
Scientific Breakthroughs in Nanobody Engineering
Deciphering the "Compactness" Bimodal Distribution
Unlike conventional antibodies, nanobodies exhibit a bimodal distribution of CDR3 compactness. TNP reveals that both "compact" loops (which stabilize by folding over the FR2) and "extended" loops are equally present in clinical data, suggesting that therapeutic design need not be biased toward a single conformational subtype.
Predicting Aggregation and Non-Specific Binding
By validating in silico profiles against 108 experimental datasets, TNP accurately flags high-risk candidates. Red flags in CDR3 compactness and surface positive charge often correlate with poor performance in BVP-ELISA and HIC assays, allowing for the rapid filtration of suboptimal binders.
Tetrad-CDR3 Co-Optimization
TNP highlights the critical role of hydrophobic and aromatic interactions between CDR3 residues and the conserved FR2 tetrad (positions 42, 49, 50, and 52). Co-optimizing these positions using TNP leads to nanobodies with superior structural stability and better developability profiles.
TNP on Tamarind Bio: Professional Nanobody Profiling
Tamarind Bio provides a high-performance environment to execute TNP’s structural analysis and surface mapping workflows without manual software configuration.
Integrated Modeling: Automatically generate 3D structures using NanoBodyBuilder2 as part of the profiling pipeline.
High-Throughput Scoring: Profile entire libraries of nanobody candidates in seconds to identify leads with "all-green" developability metrics.
How to Use TNP on Tamarind Bio
Access the Platform: Log in to tamarind.bio and select the TNP tool.
Input Sequence: Provide the primary amino acid sequence of your nanobody (VHH).
Run Structural Modeling: The platform uses NanoBodyBuilder2 to predict the 3D coordinates and CDR3 orientation.
Evaluate Biophysical Flags: Review the per-residue hydrophobicity and charge patches mapped directly onto the structure.
Compare Against Clinical Data: Check your candidate's scores against the distribution of 36 clinical-stage nanobodies to identify potential liabilities.
Export & Validate: Download high-resolution developability reports and structural models to prioritize your best leads for synthesis and wet-lab testing.