The instability index (II) predicts whether a protein will be stable in a test tube based on its amino acid sequence. Developed by Guruprasad and colleagues in 1990, it remains one of the most widely used sequence-based stability predictors in protein science.
The method works by analyzing dipeptide patterns—pairs of consecutive amino acids—that occur more frequently in unstable proteins. A low instability index suggests the protein will remain intact during expression, purification, and storage. A high value warns that the protein may degrade quickly.
For a comprehensive analysis that includes instability index along with molecular weight, pI, and other properties, use our Protein Parameters calculator.
The calculation assigns a weight value to each of the 400 possible dipeptide combinations based on how often they appear in unstable versus stable proteins. These weights are called Dipeptide Instability Weight Values (DIWV).
The instability index is computed as:
Where is the sequence length and is the instability weight for the dipeptide at position .
The DIWV values were derived from statistical analysis of 12 unstable and 32 stable proteins. Dipeptides that appeared significantly more often in unstable proteins received higher weight values.
Some dipeptides strongly destabilize proteins (high DIWV), while others are neutral or stabilizing (low or negative DIWV). The sum of all dipeptide contributions, normalized by sequence length, produces the final index.
The output table shows one row per input sequence with columns for protein ID, sequence length, and instability index.
The threshold of 40 separates stable from unstable predictions:
Most well-folded globular proteins have instability indices between 20 and 40. Values below 20 suggest very stable proteins, while values above 50 indicate likely degradation issues.
.fasta, .fa, .fas, .pdb, .csv, and .txt file uploadsThe instability index helps guide protein production and engineering decisions:
The instability index was developed from a small dataset (44 proteins) and is based on in vivo stability data. Keep these limitations in mind:
We recommend using the instability index as one factor among several when evaluating protein stability. Experimental validation remains essential for critical applications.
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
Calculate protein molecular weight (MW) from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV sequence input, average or monoisotopic masses, initiator Met removal, and disulfide correction.
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.
The instability index (II) predicts whether a protein will be stable in a test tube based on its amino acid sequence. Developed by Guruprasad and colleagues in 1990, it remains one of the most widely used sequence-based stability predictors in protein science.
The method works by analyzing dipeptide patterns—pairs of consecutive amino acids—that occur more frequently in unstable proteins. A low instability index suggests the protein will remain intact during expression, purification, and storage. A high value warns that the protein may degrade quickly.
For a comprehensive analysis that includes instability index along with molecular weight, pI, and other properties, use our Protein Parameters calculator.
The calculation assigns a weight value to each of the 400 possible dipeptide combinations based on how often they appear in unstable versus stable proteins. These weights are called Dipeptide Instability Weight Values (DIWV).
The instability index is computed as:
Where is the sequence length and is the instability weight for the dipeptide at position .
The DIWV values were derived from statistical analysis of 12 unstable and 32 stable proteins. Dipeptides that appeared significantly more often in unstable proteins received higher weight values.
Some dipeptides strongly destabilize proteins (high DIWV), while others are neutral or stabilizing (low or negative DIWV). The sum of all dipeptide contributions, normalized by sequence length, produces the final index.
The output table shows one row per input sequence with columns for protein ID, sequence length, and instability index.
The threshold of 40 separates stable from unstable predictions:
Most well-folded globular proteins have instability indices between 20 and 40. Values below 20 suggest very stable proteins, while values above 50 indicate likely degradation issues.
.fasta, .fa, .fas, .pdb, .csv, and .txt file uploadsThe instability index helps guide protein production and engineering decisions:
The instability index was developed from a small dataset (44 proteins) and is based on in vivo stability data. Keep these limitations in mind:
We recommend using the instability index as one factor among several when evaluating protein stability. Experimental validation remains essential for critical applications.
Calculate the aliphatic index of protein sequences. A measure of the relative volume occupied by aliphatic side chains, indicating thermostability.
Calculate the molar extinction coefficient of protein sequences at 280 nm. Used for protein concentration determination by UV spectroscopy.
Find potential N-linked glycosylation sites (NX[S/T] sequons) in protein sequences. Identifies asparagine residues in the consensus motif for N-glycosylation.
Calculate the GRAVY (Grand Average of Hydropathy) score of protein sequences. Positive values indicate hydrophobic proteins, negative values indicate hydrophilic proteins.
Calculate protein molecular weight (MW) from amino acid sequences in Daltons and kilodaltons. Supports FASTA and CSV sequence input, average or monoisotopic masses, initiator Met removal, and disulfide correction.
Calculate the theoretical isoelectric point (pI) of protein sequences. The pI is the pH at which a protein carries no net electrical charge.
Analyze amino acid composition of protein sequences. The tool accepts FASTA sequences and outputs the percentage of each amino acid in the sequence.
Scan protein sequences for biologically important motifs including glycosylation sites, phosphorylation sites, nuclear localization signals, prenylation motifs, and more.
Download InterPro protein family and domain records as JSON by InterPro ID.
Download QuickGO Gene Ontology term records as JSON by GO ID.