ProtPIC (Protein and Peptide Isoelectric Point Calculator) is a machine-learning-based bioinformatics tool designed to predict the isoelectric point (pI) of proteins and peptides, as well as residue-level pKa values. The tool automatically identifies input sequence type: short sequences (<=60 aa) use the peptide model and require only amino acid sequences; long sequences (>60 aa) use the protein model, which incorporates structural features (RSA, pLDDT, and secondary structure) into the calculation.
The page returns the predicted pI, and for proteins, it also returns pKa values of charged residues.
1. Amino Acid Sequences (up to 10 FASTA entries):
Parsed sequences: 0, total residues: 0
Technical Highlights
- Structural feature fusion: integrates RSA (relative solvent accessibility), pLDDT (structure confidence), and secondary-structure features
- Physical-prior integration: incorporates Henderson-Hasselbalch theoretical estimates as features
- High-accuracy prediction: pKa prediction MAE = 0.338 pH; protein pI prediction MAE = 0.581 pH; peptide pI prediction MAE = 0.118 pH
Model Performance Metrics
Performance Comparison (vs IPC 2.0)
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[pKa Prediction] Rosetta dataset, 260 residues
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Metric IPC 2.0 ProtPIC (ours)
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MAE 0.3364 0.3011
RMSE 0.5762 0.6589
Outliers (>0.5) 54(20.8%) 36(15.9%)
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[Protein pI Prediction] 581 proteins, IPC2.protein.svr.19
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Metric IPC 2.0 ProtPIC (ours)
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MAE 0.5906 0.5760
RMSE 0.8479 0.8356
R² 0.5934 0.6077
Outliers (>0.5) 247(42.5%) 232(39.9%)
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[Peptide pI Prediction] 29,774 peptides, IPC2.peptide.Conv2D
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Metric IPC 2.0 ProtPIC (ours)
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MAE 0.1216 0.118
RMSE 0.2216 0.228
R² 0.9761 0.975
Outliers (>0.25) 2691(9.0%) 2878(9.7%)
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Performance by pKa / pI range
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[pKa] ProtPIC (ours), 257 residues
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pKa Range Count MAE RMSE Outliers (>0.5)
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pKa < 4 89 0.239 0.557 13 (14.6%)
pKa 4-6 70 0.231 0.484 7 (10.0%)
pKa 6-8 24 0.345 0.616 4 (16.7%)
pKa 8-10 7 0.646 0.777 4 (57.1%)
pKa > 10 36 0.494 1.065 8 (22.2%)
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[Protein pI] ProtPIC (ours), 581 proteins
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pI Range Count MAE RMSE Outliers (>0.5)
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Acidic (<5) 156 0.560 0.814 64 (41.0%)
Neutral (5-7) 328 0.454 0.676 101 (30.8%)
Basic (7-9) 76 0.916 1.164 48 (63.2%)
Very Basic (>9) 21 1.376 1.531 19 (90.5%)
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[Peptide pI] ProtPIC (ours), 29,774 peptides
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pI Range Count MAE RMSE Outliers (>0.25)
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Very Acidic (<4) 4,578 0.064 0.098 130 (2.8%)
Acidic (4-5) 9,879 0.087 0.156 330 (3.3%)
Neutral-Acidic (5-6) 2,160 0.323 0.423 1167 (54.0%)
Neutral (6-7) 7,297 0.145 0.273 818 (11.2%)
Basic (7-9) 5,795 0.099 0.230 373 (6.4%)
Very Basic (>9) 65 0.534 0.630 60 (92.3%)
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Last updated: 2026-05-13
References
Kozlowski LP. IPC 2.0: prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res. 2021 Jul 2;49(W1):W285-W292. doi: 10.1093/nar/gkab295. PMID: 33905510; PMCID: PMC8262712.