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MALISAM

http://prodata.swmed.edu/malisam

Description :
Manual alignments for structurally analogous motifs in proteins

MegaMotifbase

http://caps.ncbs.res.in/MegaMotifbase/index.html

Description :
Structural motifs in protein families and superfamilies

Minimotif Miner

http://mnm.engr.uconn.edu/

Description :
Search tools for short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules

Phospho.ELM

http://phospho.elm.eu.org/

Description :
PhosphoBase is a database of experimentally verified phosphorylation sites and associated protein kinases. The data are collected from literature and the SwissProt database and stored in a relational SQL database. Version 3.0 contains 1766 phosphorylated residues with 1310 protein kinase annotations. PhosphoBase is available on the World Wide Web from the CBS Server at http://www.cbs.dtu.dk/databases/PhosphoBase

References :
1. Diella F, Cameron S, Gemünd C, Linding R, Via A, Kuster B, Sicheritz-Pontén T, Blom N, Gibson TJ. (2004) Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics 5:79
2. Diella F, Gould CM, Chica C, Via A, Gibson TJ. (2007) Phospho.ELM: a database of phosphorylation sites update 2008. Nucleic Acids Res. Epub Oct 25, 2007

PhylomeDB

http://phylomedb.bioinfo.cipf.es/

Description :
Experimentally validated and predicted serine phosphorylation sites in Arabidopsis thaliana

PrDOS

http://prdos.hgc.jp/cgi-bin/top.cgi

Description :
PrDOS (Protein Disorder Prediction Server) is a server to predict the disordered regions of a protein from its amino acid sequence.

BSDD

http://iris.physics.iisc.ernet.in/bsdd/

Description :
BSDD (Biomolecules Segment Display Device) searches for and displays user defined sequence motifs in known protein structures. This web based tool incorporates the graphics package of RASMOL for visualization.

FoldMiner and LOCK 2

http://foldminer.stanford.edu/

Description :
FoldMiner aligns a user-supplied or identified query structure to a database of single domain targets to discover structural neighbours and characteristic motifs. Query structures can also be aligned to one or more user-specified structures using the LOCK 2 algorithm.

iMOT

http://caps.ncbs.res.in/imot/iMOTserver.html

Description :
iMOT (interacting MOTif) server is designed to search for spatially interacting motifs among proteins sharing similar 3-dimensional structures.

Blocks WWW Server

http://blocks.fhcrc.org/

Description :
The Blocks WWW server provides tools to search DNA and protein queries against the Blocks database of multiple alignments, which represent conserved protein regions.

Cascade PSI-Blast

http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html

Description :
Cascade PSI-BLAST detects distant protein similarities using a cascade search protocol where PSI-BLAST searches are carried out on each hit, until no new hits are found in the selected database (SwissProt, SCOP, or Pfam).

DILIMOT

http://dilimot.embl.de/

Description :
Discovery of Linear Motifs (DILIMOT) is a server for finding short (3-8 amino acids) over-represented peptide patterns in a set of proteins.

ELM

http://elm.eu.org/

Description :
Eukaryotic Linear Motif (ELM) resource is a tool for predicting eukaryotic protein functional sites that report domains, motifs, and sequence patterns based on the input sequence.

GraBCas

http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/software/index.html

Description :
GraBCas is a tool for predicting granzyme B and caspase cleavage sites.

InterPro

http://www.ebi.ac.uk/interpro/index.html

Description :
Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.

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