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.

CD-Search - (Found July 8, 2008 )

CD-Search allows the user to search the Conserved Domain Database (CDD) for conserved structural and functional domains in a sequence of interest; links to 3-D structures where applicable.
http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi

Blocks WWW Server - (Found July 8, 2008 )

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

BindN - (Found July 8, 2008 )

BindN takes an amino acid sequence as input and predicts potential DNA or RNA-binding residues using support vector machines (SVMs).
http://bioinformatics.ksu.edu/bindn/

AliWABA - (Found July 8, 2008 )

Alignment on the with an A-Bruijn Approach (AliWABA) is a web based version of a method for multiple sequence alignment that represents an alignment as a directed graph and has proved useful in aligning nucleotide and amino acid sequences that are composed of repeated and shuffled subsequences.
http://aba.nbcr.net/

AlgPred - (Found July 8, 2008 )

AlgPred predicts allergenic proteins and maps IgE epitopes on allergenic proteins using several different approaches.
http://www.imtech.res.in/raghava/algpred/

AD-ENM - (Found July 8, 2008 )

Analysis of Dynamics of Elastic Network Model (AD-ENM) predicts the conformational changes a given protein structure can undergo.
http://enm.lobos.nih.gov

3Motif - (Found July 8, 2008 )

3Motif is a tool for visualizing protein sequence motifs and their properties in 3 dimensions from PDB structure files.
http://3motif.stanford.edu/

3Matrix - (Found July 8, 2008 )

3Matrix is a tool for visualizing protein sequence motifs and their properties in 3 dimensions. This tool needs to be downloaded and run locally on your own machine.
http://motif.stanford.edu/distributions/3matrix/

DOUTfinder - (Found July 8, 2008 )

Domain Outlier Finder (DOUTfinder) is a tool for facilitating protein domain detection among remotely related protein sequences.
http://mendel.imp.ac.at/dout/

ELM - (Found July 8, 2008 )

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.
http://elm.eu.org/