{"id":12,"date":"2012-02-11T15:04:28","date_gmt":"2012-02-11T15:04:28","guid":{"rendered":"http:\/\/.\/?page_id=12"},"modified":"2018-03-20T20:56:36","modified_gmt":"2018-03-20T20:56:36","slug":"pb-svindex","status":"publish","type":"page","link":"https:\/\/pbpred-us2b.univ-nantes.fr\/pentapept\/?page_id=12","title":{"rendered":"PB-SVindex"},"content":{"rendered":"
Last update on Tuesday, March 20, 2018<\/div>

Knowledge-based calculation of Structural Variability Indices (SVI) of pentapeptide sequences<\/h3>\n

This tool uses the knowledge of local conformations of pentapeptides in terms of PBs from PB-PENTAdb<\/a> database to calculate a structural variability index (SVI) for each of them. It shows if a pentapeptide is observed to have multiple local conformations in terms of PBs or not.<\/p>\n\n\n
This proposed index is similar to the Simpson’s diversity index<\/strong> used in population genetics :<\/p>\n

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pi<\/em> is the fraction of all organisms which belong to the i<\/em>-th species<\/p>\n

Here we calculate SVI using an approximation of Simpson’s index :<\/p>\n

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

Assigned variability index values vary between 0 and 1. Lower values indicate sequences with low structural variability, higher values indicate higher structural variability.\n<\/td>\n

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PB-SVindex submission form<\/h3>\n

Provide your amino acid sequences in fasta format (max 1000 sequences) :<\/strong><\/p>\n

PB-SVI is currently under maintenance. We apologize for the inconvenience. It will be back soon.<\/p><\/blockquote>\n

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