Static structure scoring
Residue and region aggregation propensity with FreeSASA accessibility.
Map aggregation-prone regions on a structure
Score residues in a protein structure, locate contiguous positive-score regions, and review surface accessibility alongside aggregation propensity.
Choose an approach
Scientific approaches
Select the analysis that best matches your scientific question. Each approach opens with its relevant inputs and controls.
Prepare
Protein structures
Start from a Structures Dataset whose rows reference PDB files with supported protein chains.
- PDB structure with standard protein residues
- Optional single-chain selection
- Up to 4 structures and 8 MB total input per analysis
Structure Artifact
chemical/x-pdbTypical neighborhood
10 ÅHow 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.
Neighborhood distance
1–30 Å
Set the Cα distance used to accumulate neighboring residue contributions.
Structure scope
All chains or one PDB chain
Score the complete supported structure or focus on a single chain.
Residue scale
Canonical or pH-adjusted
Optionally apply a pH-dependent residue propensity scale.
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
- Positive A3D scores identify aggregation-prone residues; negative values indicate aggregation-resistant local environments.
- The surface component reflects solvent exposure, while the neighborhood component reflects nearby aggregation-prone residues in 3D.
- Prioritize contiguous positive regions and inspect their structural context instead of relying on the total score alone.
1
Residue propensity map
Scan aggregation scores in structure order with positive hotspots highlighted.
2
Contiguous positive regions
Prioritize stretches of positive-scoring surface residues.
3
Chain-level summary
Compare minimum, maximum, mean, and total scores across chains.
Continue your analysis
Use a complementary method on the same Project data.
Method scope and limitations
- This method performs static Aggrescan3D scoring with FreeSASA accessibility.
- It does not run conformational-ensemble or FoldX mutation analysis.
