BiSMM | Bioinformatique Structurale et Modélisation Moléculaire

PRDB is a tool for large-scale analysis of protein tandem repeats. It includes tandem repeats detected by T-REKS program (Jorda and Kajava. Bioinformatics. 2009 25:2632) and is maintained by CRBM-CNRS, Montpellier. PRDB is designed for scientists interested in the structure, function and evolution of proteins with tandem repeats.
Comments and suggestions should be sent to: andrey.kajava@crbm.cnrs.fr

2380528 repeats found in 836670 proteins of NR release of Feb,10 2010 containing 6515100 sequences.
2210 repeats found in 1032 proteins of PDB release of Mar,23 2009 containing 45914 sequences.
103370 repeats found in 33151 proteins of SwissProt release of Feb,16 2009 containing 364403 sequences.

PRDB allows selection criteria based upon type of the sequence database (PDB, SwissProt, NR), taxonomic group, organism, number of repeats in tandem arrays, repeat length, length of protein sequence, length of tandem repeat region, structure-forming potential (TOP-IDP index), level of repeat perfection (Psim) and other parameters. The results are visualized in lists, for which various sorting options and tools of analysis are available (see details)

QueryBox

There is no query saved.

Database

Kingdom

Organism

Number of repeats from: to:

Repeat unit length from: to:

Tandem region length from: to: 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).

Structure forming potential 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)

Level of perfection 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.

Motif in the consensus pattern 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.

Protein length from: to:

Keyword

Subcellular localization

Molecular function

Pfam domains

Gi-ref 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.

Output format