Bioinformatics Links Directory : Domains and Motifs

This section includes links to tools which can give information about protein domains and/or predict motifs, domains, and patterns in peptide sequences.

ProTeus - (Found July 8, 2008 )

ProTeus (Protein Terminus) is an archive of functional signatures in protein termini
http://www.proteus.cs.huji.ac.il/index.php

ProKware - (Found July 8, 2008 )

ProKware is a tool for investigating protein structural properties such as domains, functional sites, and post-translational modifications. To use some features a stand-alone piece of software is necessary; currently available for windows only.
http://prokware.mbc.nctu.edu.tw/

SCANMOT - (Found July 8, 2008 )

SCANMOT is a sequence similarity searching tool that adds the additional constraints of simultaneous matching of multiple motifs.
http://caps.ncbs.res.in/scanmot/scanmot.html

ScanProsite - (Found July 8, 2008 )

ScanProsite is a tool for detecting PROSITE signature matches in protein sequences. Users can also search protein databases for specific motifs.
http://us.expasy.org/tools/scanprosite/

SEARCHPKS - (Found July 8, 2008 )

SEARCHPKS is a program for the detection and analysis of Polyketide Synthase (PKS) domains.
http://www.nii.res.in/searchpks.html

SEARCHGTr - (Found July 8, 2008 )

SEARCHGTr is a tool for the analysis of glycosyltransferases (GTrs) that allows you to compare a query sequence with the sequences of characterized GTrs.
http://www.nii.res.in/searchgtr.html

SCOP - (Found July 8, 2008 )

Structural Classification of Proteins - database created by a combination of manual inspection and automated methods.
http://scop.mrc-lmb.cam.ac.uk/scop/

Scooby-domain - (Found July 8, 2008 )

Scooby-domain (sequence hydrophobicity predicts domains) is a method to identify globular domains in protein sequence, based on the observed lengths and hydrophobicities of domains from proteins with known tertiary structure.
http://ibivu.cs.vu.nl/programs/scoobywww/

Scansite - (Found July 8, 2008 )

Scansite searches for motifs within proteins that are likely to be phosphorylated or that bind to common cellular signaling domains.
http://scansite.mit.edu/

ProFunc - (Found July 8, 2008 )

ProFunc takes a PDB-format structure as input and predicts the likely function of the protein based on various sequence and structural analysis methods.
http://www.ebi.ac.uk/thornton-srv/databases/ProFunc/