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ADDA - A Domain Database

http://ekhidna.biocenter.helsinki.fi/sqgraph/pairsdb

Description :
ADDA is a global clustering of protein sequences into protein domains and protein domain families. The database currently contains domains for 1.5 Mio sequences from UniProt, ENSEMBL, and other sequence databases. The domains are grouped into 123,000 families of which 40,000 have more than five members. The database is built in an entirely automated fashion and is updated regularly. The data is available for download and for querying via the WWW.

References :
Heger A. and Holm L.(2003) Exhaustive enumeration of protein domain families. J Mol Biol. 328: 749-767.

DIMA

http://mips.gsf.de/genre/proj/dima2

Description :
Domain interaction map: experimental and predicted protein domain interactions

DOMINE

http://domine.utdallas.edu/

Description :
Known and predicted protein domain interactions observed in PDB entries,

PepCyber:P~Pep

http://pepcyber.umn.edu/PepCyber

Description :
Human protein interactions mediated by phosphoprotein-binding domains

PhosPhAt

http://phosphat.mpimp-golm.mpg.de/app.html

Description :
Arabidopsis Protein Phosphorylation Site Database

ExDom

http://66.170.16.154/ExDom/

Description :
Exon-intron structure of protein domains in seven eukaryotic genomes

DICHROWEB

http://public-1.cryst.bbk.ac.uk/cdweb/html/

Description :
A server that supports several different algorithms for the analysis of Circular Dichroism (CD) spectra for the prediction of protein secondary structure. Results also contain a graphical comparison of calculated versus experimental results.

DisEMBL

http://dis.embl.de/

Description :
A computational tool for prediction of disordered/unstructured regions within a protein sequence.

DSSPcont

http://cubic.bioc.columbia.edu/services/DSSPcont/

Description :
DSSPcont automates protein secondary structure prediction from PDB structures to reflect structural variations due to thermal fluctuations.

GlobPlot

http://globplot.embl.de/

Description :
GlobPlot has the ability to plot the tendency towards globularity for a given protein sequence. Can also perform SMART/Pfam domain prediction.

Jpred 3

http://www.compbio.dundee.ac.uk/jpred

Description :
Jpred 3 is an improved web server for predicting protein secondary structure in three states (alpha helix, beta strand and coil). Improvements include better usability, batch submission of sequences and updates to the search databases.

NORSp

http://cubic.bioc.columbia.edu/services/NORSp/

Description :
NORSp (predictor of NOn-Regular Secondary Structure) is a tool for predicting disordered regions in proteins.

Protein Peeling

http://www.ebgm.jussieu.fr/~gelly/index.html

Description :
Protein Peeling is an approach for splitting a protein three dimensional (3D) structure into protein units, an intermediate level of protein structure description between protein domains and secondary structures.

PSA

http://bmerc-www.bu.edu/psa/request.htm

Description :
Prediction of probable secondary structures and fold-class; good for visualizing amphipathic helices, where present.

RbDe

http://icb.med.cornell.edu/crt/RbDe/index.xml

Description :
Residue-based Diagram editor (RbDe) constructs schematic diagrams of protein sequences to help observe the topology of secondary structure and transmembrane regions; free registration is required to use all features.

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