Instability Index

How to calculate the protein instability index?

Paste a protein sequence or upload a FASTA file, then select Generate. The calculator reports one row per sequence: protein ID, amino acid count, instability index, and predicted stability. It uses the Guruprasad dipeptide method, with Stable below 40 and Unstable at or above 40. The score is dimensionless.

Human ubiquitin

Load the bundled example or paste this 76-residue sequence:

>Human_ubiquitin
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGG

The result agrees with an independent calculation using Biopython's ProtParam implementation. Stable is the prediction from this sequence descriptor; it does not guarantee successful expression, resistance to unfolding, or storage stability.

Compare sequences

Each FASTA record needs a header followed by sequence data on separate lines:

>alpha
PEPTIDE
>beta
ACDEFGHIKLMNPQRSTVWY

These short sequences demonstrate the calculation. Their classifications have limited biological meaning because they contain few dipeptides. Each record is calculated separately, with no pair formed across record boundaries.

Input

Guest runs accept up to 5 sequences, free accounts up to 100, and paid plans have no sequence-count cap. These limits apply to the entire run.

Put names and descriptions after >. A plain-text name such as GFP consists of valid amino acid letters and would become sequence data. In >sample kinase, the word kinase stays in the header and does not affect the score. Empty FASTA records and sequence text before the first header cause an error. A compact record such as >sample ACDE needs its sequence moved to the next line.

PDB input always produces a warning: coordinates can omit residues, especially at the termini, so its score may differ from the complete protein sequence. Use full-length FASTA when comparing complete proteins. Raw database annotations and FASTQ records are not accepted as pasted protein sequences. CSV to FASTA provides explicit column selection for tables with other layouts, and PDB to FASTA offers control over sequence extraction.

Settings and results

There are no calculation settings. All sequences use the same dipeptide weights and threshold.

The table supports sorting and searching. Its download control exports the results as CSV, JSON, or Excel. Use distinct header identifiers to distinguish records, especially when several headers share a pipe-delimited prefix.

How does the instability index work?

The Guruprasad method was derived from 12 unstable and 32 stable proteins. It assigns a dipeptide instability weight value (DIWV) to each of the 400 ordered pairs of standard amino acids:

Here, $L$ is sequence length. Only consecutive residues within a record contribute; there is no closing pair from the last residue to the first. Negative weights can produce a negative index, which is a valid numerical result.

The calculation follows the ExPASy ProtParam convention. An index below 40 predicts stability; a higher index suggests instability. This calculator assigns the boundary value of 40 to Unstable. The weights describe statistical associations, not a physical destabilizing energy for each pair.

What can the score tell me?

The instability index is an empirical sequence descriptor. It does not calculate folding free energy, melting temperature, aggregation, solubility, or degradation half-life in hours. Buffer composition, pH, temperature, modifications, cofactors, and experimental conditions are absent from the calculation. A lower score does not establish a longer shelf life or a better protein variant.

For a broader property report, Protein Parameters includes molecular weight, pI, and additional descriptors. Protein Stability compares separate sequence indicators; its instability classification also belongs only to this method. Neither replaces experimental measurement of the stability endpoint you care about.

FAQ

Why are gaps and unknown amino acids rejected?

The weight table covers only the 20 standard amino acids. Removing a gap or unknown residue would create a new adjacent pair and change the index. Provide an ungapped sequence with resolved residues instead.

Does an instability index above 40 mean my protein will degrade quickly?

It is an instability prediction from the dipeptide method. It does not specify a degradation rate or half-life under your experimental conditions, and it cannot predict storage duration.

Can I calculate an index for a peptide?

The calculator accepts two or more amino acids. Very short sequences give a score dominated by only a few dipeptides, so treat their classification cautiously.