Domains
From MyBio
This article concerns protein domains.
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CDD is a protein sequence searchable conserved domain database for interactive domain family analysis, whose pre-computed results are available as the âConserved Domainâ links in Entrez. Protein query sequences submitted to NCBI's protein BLAST search service are scanned for conserved domain signatures by default. The CDD collection contains models imported from Pfam, SMART and COG, as well as domain models curated at NCBI. 
EVEREST is a collection of evolutionary conserved protein domains. A system which attempts to idenitfy and classify protein domains into families automatically using protein sequence alone, defining 20,000 families by one or more HMMs. Allows advanced seqeunce-based searching and analyses relationships between, within and across domain families, and graphical visualization of domain organisation.
Protein Domain Profile Analysis
Search a library of profiles with a protein sequence.
ProDom
Protein Domain Database.
InterPro database: Database of protein families
This is an manually integrated resource for proteins with data from PROSITE, Pfam, PRINTS, ProDom, SMART, TIGRFAMs, PIR SuperFamily, the structure-based SUPERFAMILY and are available in InterPro for text- and sequence-based searching.
ProtoNet
Automatic hierarchical classification of the protein space. The ProtoNet 3.0 database, developed at The Hebrew University of Jerusalem, includes over a million proteins organized in a hierarchical tree of protein clusters. Clusters quality is validated and each family is associated with rich statistical information. Interactive navigation tools facilitate tracing protein families, subfamilies and suprfamilies. ProtoNet allows analysis your protein sequence in view of the clustering tree.
PRINT db
Groups of conserved motifs used to characterise protein families.
Biozon Domain Prediction
Automatic prediction of protein domains from sequence information using a hybrid learning system. We describe a novel method for detecting the domain structure of a protein from sequence information alone. The method is based on analyzing multiple sequence alignments that are derived from a database search. Multiple measures are defined to quantify the domain information content of each position along the sequence and are combined into a single predictor using a neural network. The output is further smoothed and post-processed using a probabilistic model to predict the most likely transition positions between domains. The method was assessed using the domain definitions in SCOP and CATH for proteins of known structure and was compared with several other existing methods. Our method performs well both in terms of accuracy and sensitivity. It improves significantly over the best methods available, even some of the semi-manual ones, while being fully automatic. Our method can also be used to suggest and verify domain partitions based on structural data. A few examples of predicted domain definitions and alternative partitions, as suggested by our method, are also discussed.
SMART: Main page
SMART: Main page. Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95,Letunic et al. (2006) Nucleic Acids Res 34,Select your default SMART mode. You can use SMART in two different modes: normal or genomic.The main difference is in the ...
TIGRFAMs Home Page
TIGRFAMs are protein families based on Hidden Markov Models or HMMs. Use this page to see the curated seed alignmet for each TIGRFAM, the full alignment of all family members and the cutoff scores for ...
ADDA Domain database
ADDA - Automatic Domain Decomposition Algorithm. Home. Sequence. Family. Browse. Genomes. Statistics. Download. Help. ADDA - Automatic decomposition of domain families Summary This is a web interface for ADDA, an automatic algorithm for ...
Gene3D - Structural and Functional Annotation of Protein Families.
Searching with an NCBI Taxon IDs (e.g. 9606) will return a summary of annotation and links to downloadable files containing complete Gene3D annotation for that species.
SBASE - Support Vector Machines Domain Prediction System
Tool facilitates the detection of domain homologies based on sequence database search. Library of protein domain sequences contains 1m protein sequence segments annotated by structure, function, ligand-binding or cellular topology, clustered into groups.
DOUTfinder
Facilitates protein domain detection among related protein sequences in the twilight zone of sequence similarity, allowing detection of non-trivial domain relationships and insights into the function and evolution of distantly related sequence families.
