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Created on: 26-Oct-2012   Last updated on: 26-Oct-2012  |  How to cite this?
Total resources - 25
A list of resources for protein domains
Akhilesh Bajpai and Sravanthi Davuluri (Correspondence: Acharya KK, kshitish@ibab.ac.in)

Resources
Short description*Rank by usage frequency Click to Edit / Add comments
SMART - Simple Modular Architecture Research Tool
http://smart.embl-heidelberg.de
A resource that allows the identification and annotation of genetically mobile domains and the analysis of domain architectures
1
InterPro
http://www.ebi.ac.uk/interpro
A resource providing functional analysis of protein sequences by classifying them into families and predicting the domains and sites
66
Pfam
http://pfam.sanger.ac.uk
A collection of protein families, each represented by multiple sequence alignments and hidden Markov models
66
DIAL - Domain Identification Algorithm
http://caps.ncbs.res.in/DIAL
A web server for the identification of structural domains using the three-dimensional coordinates of a protein
75
PROSITE
http://prosite.expasy.org
A database of protein domains, families and functional sites from ExPASy
76
CDD - Conserved Domain Database
http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
A resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins
88
PANDIT - Protein and Associated Nucleotide Domains with Inferred Trees
http://www.ebi.ac.uk/goldman-srv/pandit
A collection of multiple sequence alignments and phylogenetic trees covering the common protein domains
92
MyHits
http://myhits.isb-sib.ch
A database of protein domains and also includes tools for the investigation of the relationships between protein sequences and motifs
94
CATH - Classification of Protein Structures
http://www.cathdb.info
A resource for manually curated classification of protein domain structures
96
SCOP - Structural Classification of Proteins
http://scop.mrc-lmb.cam.ac.uk/scop
A database for classification of protein structural domains based on structure and sequence similarities
96
ADDA - Automatic Domain Decomposition Algorithm
http://ekhidna.biocenter.helsinki.fi/sqgraph
An automatic algorithm for clustering of all protein domain families
97
2ZIP
http://2zip.molgen.mpg.de
A program to predict Leucine zipper domains in the given amino acid sequence
100
DHcL - Domain Hierarchy and closed Loops
http://sitron.bccs.uib.no/dhcl
A server that calculates domain structures at different levels of energy hierarchy and elements of the loop-n-lock structure, closed loops and vanderWaals locks
100

URL not working as on 15 Nov 2016 (confirmed on 23 Feb 2017)
DoBo
http://sysbio.rnet.missouri.edu/dobo
A server for protein domain predictions by integrating homology modeling and machine learning
100
DOMAINATION
http://www.ibi.vu.nl/programs/domainationwww
A method to identify domains in a protein sequence based on PSI-BLAST similarity searches
100
DomIns - Database of Domain Insertions
http://www.domins.org
A resource for domain insertions in known protein structures
100
DomPred
http://bioinf.cs.ucl.ac.uk/dompred
A server for prediction of putative protein domains for a given protein sequence using various methods including similarity search to Pfam-A domain sequences
100
DOUTfinder
http://mendel.imp.ac.at/dout
A web-based tool for protein domain detection among related protein sequences based on sequence similarity
100
fastSCOP
http://gemdock.life.nctu.edu.tw/fastSCOP
A web server that identifies the structural domains of a query protein structure, using 3D-BLAST tool and the SCOP database
100
InterDom - Database of Interacting Domains
http://interdom.i2r.a-star.edu.sg
A database of putative interacting protein domains derived from multiple sources
100
PLecDom
http://www.nipgr.res.in/plecdom.html
A program for detection and analysis of the plant lectin domains in a given polypeptide or EST sequence
100
ProDom
http://prodom.prabi.fr
A database that has protein domain families generated from the UniProt Knowledge Database by sequence comparison
100
Scooby-domain - Sequence hydrophobicity predicts domains
http://www.ibi.vu.nl/programs/scoobywww
A method for identification of globular domains in protein sequences
100
TreeDomViewer
http://www.bioinformatics.nl/tools/treedom
A tool for the visualization protein domain structure and phylogeny
100

TreedomViewer service has been discontinued, as on 15 Nov 2016 (confirmed on 23 Feb 2017)
WDAC - Weighted Domain Architecture Comparison Tool
http://pat.kobic.re.kr/wdac/index.htm
A web-server for performing protein homology search by comparing protein domain architectures
100
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