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PB-SVindex

PB-SVindex : knowledge-based calculation of Structural Variability Indices of pentapeptide sequences

This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from PB-PENTAdb database to calculate structural variability index (SVI) for each of them. It is a statistical index that shows if a pentapeptide is observed to have multiple local conformations in terms of PBs or not.

This proposed index is similar to the Simpson’s diversity index used in population genetics :

pi is the fraction of all organisms which belong to the i-th species

Here we calculate SVI using an approximation of Simpson’s index :

where, for a given amino acid motif, ni is its occurence in PB class i, and n is the total number of times this motif is found in the database.
This is an estimator for Simpson’s index for sampling without replacement.

Assigned variability index values vary between 0 and 1. Lower values indicate sequences with low structural variability, higher values indicate higher structural variability.

User can provide a SCOP domain ID to get the SVindex values for its sequence.


The output of this query will give a result page as follows

User can choose to provide one more protein sequences in fasta format (1000 sequences at most) as shown below


As output, a table is provided with

• first 8 characters of ID of sequence (it removes the “>” from first line)
• Number of residues in sequence
• SV index

with SVindices values separated by comas.