Protein-Sol
Predict protein solubility from sequence with feature-level and windowed profile outputs.
What is Protein-Sol?
Protein-Sol is an empirical sequence-based method for predicting protein solubility. It reports the core quantities described by the University of Manchester method: percent-sol, scaled-sol, population-sol, and predicted pI.
The method calculates sequence features such as charge balance, amino acid composition, Kyte-Doolittle hydropathy, fold propensity, disorder propensity, entropy, and beta propensity. These features are compared with the Niwa cell-free expression solubility dataset to estimate solubility.
How to use Protein-Sol online
Paste or upload protein FASTA records to run Protein-Sol online. ProteinIQ checks the identifiers and sequence lengths, runs each record with at least 21 standard amino acids unless membrane exclusion is enabled, and reports shorter records as skipped. Results include a prediction table plus downloadable feature, profile, composition, and native run files.
Inputs
| Input | Requirement |
|---|---|
Protein sequences | FASTA text or a .fasta, .fa, .fas, or .txt file. |
| Sequence length | At least one record must contain 21 standard amino acids. Shorter records are skipped and listed in the result warnings. |
| Sequence identifier | The first whitespace-delimited token of the header, including >, must be unique among processed records. Empty headers use the native identifier >. |
| Job size | Up to 25 KB. Record limits range from 5 for guests to 100 on the Pro plan. |
Use the 20 standard one-letter amino acid codes when possible:
>my_protein
MKTAYIAKQRQISFVKSHFSRQLEERLGLIEVQLRProtein-Sol ignores stop symbols and characters outside the standard amino acid alphabet during its sequence preparation step. Headers must begin with > in the first column. Protein-Sol ignores text before the first header and accepts an empty > header. For reproducible predictions, submit canonical protein FASTA records.
Settings
All options are off by default, matching the native sequence-prediction software.
| Setting | Effect |
|---|---|
| Charge histidine | Assigns histidine a charge of +1 in the feature calculations rather than the default neutral charge. |
| Exclude predicted membrane proteins | Omits sequences with a 21-residue window whose mean Kyte-Doolittle hydropathy exceeds 1.6. An entirely excluded batch can return no prediction rows. The native logs explain exclusions. |
| Export whole-sequence features | Adds whole_seq_data.txt, including full headers and native whole-sequence features. |
| Export residue properties | Adds native seq_N.txt files with per-residue properties. |
Results
The Predictions view contains the native prediction rows for processed sequences. The same rows are available in the predictions CSV.
| Column | Meaning |
|---|---|
ID | Effective FASTA identifier reported by Protein-Sol. |
percent-sol | Predicted solubility percentage. |
scaled-sol | Prediction scaled over the source reference range. |
population-sol | Reference population solubility on the same scale. |
pI | Predicted isoelectric point used by the Protein-Sol feature model. |
The CSV files view includes downloads for feature weights, feature deviations, sliding-window profiles, and whole-sequence or windowed composition data.
Downloadable Files
Protein-Sol returns CSV tables for the parsed results:
predictions.csv: solubility predictions and predicted pI.feature_weights.csv: feature contribution weights used by the model.feature_deviations.csv: sequence feature deviations.profiles.csv: 21-residue window profile values.composition.csv: whole-sequence and windowed composition features.composition_summaries.csv: composition summary lines.
Generated run files are retained with the result download bundle:
seq_prediction.txt: prediction rows, feature weights, deviations, and 21-residue profiles.seq_composition.txt: whole-sequence, 21-residue, and 51-residue composition features.run.log: execution log.messages.txt: native parser messages and diagnostics.whole_seq_data.txtandseq_N.txt: optional native exports enabled in Settings.stdout.logandstderr.log: native process output when present.
Citation
Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. Protein-Sol: a web tool for predicting protein solubility from sequence. Bioinformatics. 2017;33(19):3098-3100. doi:10.1093/bioinformatics/btx345
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