Structural Bioinformatics and Molecular Modeling
CRBM-CNRS Montpellier

from: to: repeats

from: to: res.

from: to: res.Minimal length of repeat arrays is 9 for homorepeats and 14 for other repeats with potential biological meaning (see Jorda and Kajava. Bioinformatics. 2009 25:2632).

from: to: The structure forming potential can vary from -0.5 (unstructured) to 0.5 (structured).

It is based on the TOP-IDP scale (Campen et al., Protein and Peptide Letters, 2008, 15: 956)

from: to: The level of perfection is based on Psim coefficient calculated as Hamming distances between the repeats and their consensus sequence.
In PRDB, Psim ranges from 0.7 to 1,considering that for lower values the number of false positive TRs significantly increases.

For instance, a query with Psim=1 will return only perfect repeats.

For example, gppg motif will display TRs with consensus patterns GPPG, GPPGPP, MGPPGXKGEXG. You can specify several motifs separated by “|”. For example, gppg|kdn will display TRs with consensus patterns GPPG, GPPGPP, MGPPGXKGEXG and GXKDN, DFNHX-FKDN-FSA.

from: to: residues

You can specify several gis separated by "|".
When searching for repeats in a protein with a known gi, make sure it belongs to one of the featured databases and it is correctly selected in the "database" field. For instance, "114149251|1175416" will report all the repeats found in these two proteins(only if "Swissprot" has been selected.)

Strain redundancy filter This option allows to ignore the duplicates originated from sequenced strains of the same organism.


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