Aggrescan3D

Aggrescan3D webserver overview

Aggrescan3D (A3D) estimates residue-level aggregation propensity from a protein structure. Unlike sequence-only predictors, it scores each residue in its three-dimensional context by combining the intrinsic AGGRESCAN scale with solvent exposure and neighboring residues in space.

ProteinIQ runs the static Aggrescan3D 1.1.0 workflow on one PDB structure per job. Each run returns a scored structure, a residue score table, per-chain and overall summary statistics, per-chain score plots, and the native run files.

The static pipeline computes solvent accessibility with freeSASA, applies the A3D residue scoring model within the selected distance threshold, and writes the scores into the B-factor column of the output structure.

Pricing

Each Aggrescan3D job costs a flat 5 credits. Structure size, chain selection, distance threshold, and pH do not change the price. The exact quote is shown before submission.

Inputs

Input	Accepted formats	Limits
Protein Structure	.pdb, .ent, or RCSB PDB ID	One structure per job, up to 50 MB

The structure must contain protein atoms and at least four residues with standard amino acid names in the analyzed chain or structure. HETATM MSE records also count, because native input preparation rewrites them to MET. ProteinIQ checks these rules before submission.

Settings

Parameter	Type	Default	Description
Distance threshold (Å)	integer	10	Spatial radius for neighboring residue contributions. Minimum 1. 5 emphasizes more local contributions.
Chain ID	string	All chains	One chain letter or number from the uploaded structure. Leave blank to analyze every protein chain.
pH	number	optional	pH-dependent A3D scale, greater than 0 and at most 14. Leave blank to use the native default scale.

Outputs

Tab	Contents
Structure	Scored output.pdb in the 3D viewer, with A3D scores in the B-factor column
Residues	One row per analyzed residue from A3D.csv
Summary	Average, total, minimum, and maximum A3D scores from A3D_summary.json, overall and per chain
Files	All downloadable native outputs

File	Description
A3D.csv	Residue-level A3D scores
A3D_summary.json	Summary statistics for the whole run and for each chain
output.pdb	Input structure with A3D scores written to the B-factor column
input.pdb	Normalized structure passed to Aggrescan3D
config.ini	Exact native configuration used for the run
Plot files (.png, .svg)	Per-chain residue score plots
Aggrescan.log, aggrescan_stdout.log, aggrescan_stderr.log	Native run diagnostics

Understanding results

Field	Description
Protein	Structure identifier used for the run
Chain	Chain identifier
Residue	Residue number
Residue Name	One-letter residue code
Score	Native A3D residue score
Scope	All covers every analyzed residue; other values are chain IDs
Average A3D score	Mean score across the scope, including residues with a score of zero
Total A3D score	Sum of residue scores across the scope, so it depends on how many residues were analyzed
Minimum, Maximum	Lowest and highest residue scores in the scope

Positive scores mark residues in structural environments that are more aggregation-prone. Negative scores mark residues in environments that favor solubility. Scores are not aggregation percentages or probabilities.

Use the overall average to compare structures, and compare runs only when they share the same pH, distance threshold, and chain scope. When a chain is selected, the All row covers that chain only.

Limitations

• Only the static Aggrescan3D workflow is available.
• Each job accepts one structure.
• Dynamic mode, mutation workflows, FoldX integration, automated mutation, and NACCESS are not included.