Aggrescan3D

Analyze aggregation-prone regions in a protein structure.

Input

Protein Structure

Distance threshold (Å)

5 credits

Output

Configure inputs to begin

Set options on the left, then click “Submit job”.

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 native Aggrescan3D workflow on a single PDB structure per job. The goal is to support the original static analysis outputs faithfully rather than approximate them with local scoring logic.

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 default patch-oriented analysis mode in Aggrescan3D. The 5 Å setting narrows the calculation toward more local residue contributions.

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`	Spatial radius used by the native static calculation. `10 Å` is the default patch mode. `5 Å` emphasizes more local residue contributions.

Results

The tool returns native static outputs directly:

Table: residue-level rows from A3D.csv
Files: canonical artifacts including A3D.csv, A3D_summary.json, output.pdb, and native plot images
Summary: per-chain and global score statistics parsed 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 scored PDB file can be opened in molecular viewers for structure-based inspection, while the summary JSON provides per-chain and global score statistics from the published workflow.

Limitations

This tool currently supports the static Aggrescan3D workflow only.
It accepts one structure per job.
Dynamic mode, mutation workflows, FoldX integration, and pH-dependent scoring are out of scope for this tool.
Aggrescan3D expects protein structures and may reject unsupported residue content or malformed PDB inputs.

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What is Aggrescan3D?

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 default patch-oriented analysis mode in Aggrescan3D. The 5 Å setting narrows the calculation toward more local residue contributions.

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`	Spatial radius used by the native static calculation. `10 Å` is the default patch mode. `5 Å` emphasizes more local residue contributions.

Results

The tool returns native static outputs directly:

Table: residue-level rows from A3D.csv
Files: canonical artifacts including A3D.csv, A3D_summary.json, output.pdb, and native plot images
Summary: per-chain and global score statistics parsed 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

Limitations

This tool currently supports the static Aggrescan3D workflow only.
It accepts one structure per job.
Dynamic mode, mutation workflows, FoldX integration, and pH-dependent scoring are out of scope for this tool.
Aggrescan3D expects protein structures and may reject unsupported residue content or malformed PDB inputs.