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.

EVALLER - (Found July 8, 2008 )

EVALLER predicts potential protein allergenicity from primary amino acid sequence.
http://bioinformatics.bmc.uu.se/evaller/

Motif3D - (Found July 8, 2008 )

Motif3D is a protein structure viewer for visualizing sequence motifs contained in the PRINTS database on 3D structures.
http://umber.sbs.man.ac.uk/dbbrowser/motif3d/motif3d.html

Meta-MEME - (Found July 8, 2008 )

Creates hidden Markov model of motif from MEME output and searches sequence database for matches to this motif.
http://metameme.sdsc.edu/

MAGIIC-PRO - (Found July 8, 2008 )

MAGIIC-PRO is a tool for detecting patterns in protein sequences. MAGIIC-PRO takes a protein sequence as input and helps users prepare training data for the pattern mining experiments by using Swiss-Prot annotations or by PSI-BLAST. Multiple resources for analysis of the detected patterns are also presented.
http://biominer.bime.ntu.edu.tw/magiicpro/

KinasePhos 2.0 - (Found July 8, 2008 )

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.
http://kinasephos2.mbc.nctu.edu.tw/

KinasePhos - (Found July 8, 2008 )

KinasePhos is a tool for identifying kinase-specific phosphorylation sites in protein sequences.
http://kinasephos.mbc.nctu.edu.tw/

KemaDom - (Found July 8, 2008 )

Kernal Machine for Domain Prediction (KemaDom) can predict the number of domains in a protein sequence using the local context information of neighboring amino acids.
http://www.iipl.fudan.edu.cn/~lschen/kemadom.htm

InterPro - (Found July 8, 2008 )

Integrated database of commonly used signature databases (e.g. PROSITE, PRINTS, SMART, Pfam, ProDom); text- and sequence-based searches.
http://www.ebi.ac.uk/interpro/index.html

GPS - (Found July 8, 2008 )

Using datasets of known phosphorylation sites, the Group based Phosphorylation Scoring method (GPS) allows the prediction of kinase specific phosphorylation sites from primary protein sequences.
http://973-proteinweb.ustc.edu.cn/gps/gps_web/predict.php

FunShift - (Found July 8, 2008 )

FunShift is a database that stores Pfam subfamily classification for protein domain families and analyses them for functional changes using evolutionary substitution rates and conservation shifts.
http://funshift.cgb.ki.se/