VHH structure prediction
Predict one or two 80–180-residue nanobody structures with fixed deterministic settings.
Start this methodPredict nanobody structures with NbForge
Predict VHH coordinates and inspect residue confidence, sequence conservation, and backbone geometry.
Choose an approach
Scientific approaches
Select the analysis that best matches your scientific question. Each approach opens with its relevant inputs and controls.
Prepare
Nanobody variable-domain sequences
Use one protein or annotated-sequence Dataset with an unambiguous VHH sequence column.
- One or two rows per analysis
- 80–180 unambiguous amino acids per VHH sequence
- One frozen Selection or Dataset Version
Sequence column
sequenceHow the analysis starts
Choose a Project, open a compatible Dataset, then select the rows you want to analyze. Ubi will open this method with the compatible controls and column mappings ready to review.
Configure the scientific method
These controls appear in the Dataset analysis panel, where values can be checked against the actual input before the run starts.
Sequence mapping
Dataset sequence column
Map the field containing each VHH amino-acid sequence.
Inference limits
Seed 1 · no minimization · no NbFrame scoring
This analysis predicts coordinates without minimization or NbFrame scoring.
Prediction settings
Seed 1 · deterministic inference
Keep settings fixed when comparing structures across candidates.
Review results as scientific outputs
Results open with the figures, structures, sequences, and metrics needed to answer the scientific question. Downloadable files remain available for downstream analysis.
How to interpret the result
- Coordinates and confidence values are model predictions, not experimental structures or B-factors.
- Inspect CDR3 and low-confidence regions before design decisions or experimental use.
- Compare outputs only when checkpoint, sequence, and deterministic settings are identical.
1
Predicted-structure Dataset
Compare source sequences, residue confidence, and structure links.
2
Sequence-conserving structures
Open complete single-chain VHH coordinates and inspect backbone geometry.
3
Residue confidence profile
Locate lower-confidence positions before using the model for design decisions.
Continue your analysis
Use a complementary method on the same Project data.
Method scope and limitations
- NbForge predicts VHH structures only; it does not perform minimization or NbFrame scoring.
- Coordinates and confidence values are model predictions, not experimental structures.
