Analyze aggregation-prone regions in a protein structure. Learn more
What is Aggrescan3D?
Aggrescan3D (A3D) estimates residue-level aggregation propensity from a protein structure. Unlike sequence-only predictors, it evaluates each residue in its three-dimensional context by combining the intrinsic AGGRESCAN scale with solvent exposure and nearby residues in space.
This ProteinIQ tool runs the static Aggrescan3D 1.1.0 workflow on a single PDB structure per job. It invokes the published aggrescan application and returns its analysis, structure, configuration, plot, and diagnostic files.
How does the static Aggrescan3D workflow work?
The native static pipeline performs three core steps:
- It computes solvent accessibility for the structure with
freeSASA. - It applies the Aggrescan3D residue scoring model using the native aggregation matrix and the selected distance threshold.
- It generates canonical outputs including the residue score table, per-chain score plots, a summary JSON, and a scored PDB file with scores written into the B-factor column.
The 10 Å threshold is the native default and provides a patch-oriented analysis. A 5 Å threshold narrows the calculation toward more local residue contributions. Aggrescan3D accepts other integer cutoffs when a different neighborhood radius is needed.
How to use Aggrescan3D online
Input
| Input | Description |
|---|---|
Protein Structure | One PDB structure uploaded as .pdb or .ent, or fetched from RCSB by PDB ID. Only one structure is accepted per job. |
Settings
| Setting | Description |
|---|---|
Distance threshold | Positive integer spatial radius used by the static calculation. 10 Å is the native default; 5 Å emphasizes more local residue contributions. |
Chain ID | Optional one-letter or one-number PDB chain to analyze. Leave blank to analyze every protein chain. |
pH | Optional pH-dependent A3D scale greater than 0 and at most 14. Leave blank to use the native default scale. |
Results
The tool returns native static outputs directly:
- Structure: the scored
output.pdb, with A3D values in the B-factor column - Table: residue-level rows from
A3D.csv - Files:
A3D.csv,A3D_summary.json,output.pdb, the normalizedinput.pdb,config.ini, plots, and diagnostic logs - Summary: per-chain and global score statistics from
A3D_summary.json
| Output column | Description |
|---|---|
Protein | Structure identifier used for the run |
Chain | Chain identifier |
Residue | Residue number |
Residue Name | One-letter residue code |
Score | native Aggrescan3D residue score |
Interpreting results
More positive scores indicate residues in structural environments that are more aggregation-prone. More negative scores indicate residues in environments that promote solubility. The structure viewer maps the scored PDB directly, while the downloadable input and configuration files preserve the exact native run context.
Limitations
- This tool currently supports the static Aggrescan3D workflow only.
- It accepts one structure per job.
- Dynamic mode, mutation workflows, FoldX integration, automated mutation, and NACCESS are not included.
- Aggrescan3D requires at least four residues using the 20 standard residue names in the selected chain or structure.
HETATMMSE records are also accepted because the native input preparation rewrites them to MET. ProteinIQ checks these source-specific PDB rules before submission.
