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.

SVM-PROT - (Found July 8, 2008 )

Support Vector Machine of Proteins (SVM-PROT) is a tool for predicting and classifying protein families.
http://jing.cz3.nus.edu.sg/cgi-bin/svmprot.cgi

SUMOsp - (Found July 8, 2008 )

SUMOylation Sites Prediction (SUMOsp) predicts sites for sumoylation, a reversible post-translational modification of proteins by the small ubiquitin-related modifiers (SUMO).
http://bioinformatics.lcd-ustc.org/sumosp/prediction.php

SMART - (Found July 8, 2008 )

SMART (Simple Modular Architecture Research Tool) is a web tool for the identification and annotation of protein domains, and provides a platform for the comparative study of complex domain architectures in genes and proteins.
http://smart.embl-heidelberg.de/

SledgeHMMER - (Found July 8, 2008 )

SledgeHMMER is a tool for searching the Pfam database using a parallelized version of the program hmmpfam. The user can perform queries with one or more sequences at a time and then receive the results by e-mail.
http://sledgehmmer.sdsc.edu/

SIRW - (Found July 8, 2008 )

SIRW is a web interface to SIR (Simple Indexing and Retrieval System). It combines the ability to search proteinnucleotide databases with keywords and a sequence motif.
http://sirw.embl.de/

TreeDet - (Found July 8, 2008 )

Tree Determinant (TreeDet) is a tool for predicting functional residues in protein sequence alignments.
http://www.pdg.cnb.uam.es/Servers/treedet/

QSCOP - BLAST - (Found July 8, 2008 )

QSCOP-BLAST is a service that uses BLAST to search the QSCOP (Quantitative SCOP) server, an extension of classic SCOP (Structural Classification of Proteins).
http://qscop-blast.services.came.sbg.ac.at/

RNABindR - (Found July 8, 2008 )

RNABindR is a server for analyzing and predicting RNA binding sites in proteins.
http://bindr.gdcb.iastate.edu/RNABindR/

RE-MuSiC - (Found July 8, 2008 )

RE-MuSiC is a tool for multiple sequence alignments where users can specify conserved blocks by supplying regular expression contraints.
http://140.113.239.131/RE-MUSIC/

QuasiMotiFinder - (Found July 8, 2008 )

QuasiMotiFinder uses physicochemical similarity to PROSITE motifs and evolutionary conservation to predict sequence locations with possible function (pseudo-motifs).
http://quasimotifinder.tau.ac.il/