Protein Function Analysis
PredictProtein is a service for sequence analysis, structure and function prediction. When you submit any protein sequence PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure and function
http://www.predictprotein.org/
Harvester collects and displays bioinformatic protein information and predictions for human proteins from various databases for realtime access.
http://harvester.fzk.de/harvester/
The iProClass database provides value-added information reports for UniProtKB and unique NCBI Entrez protein sequences in UniParc, with links to over 90 biological databases, including databases for protein families, functions and pathways, interactions, structures and structural classifications, genes and genomes, ontologies, literature, and taxonomy.
http://pir.georgetown.edu/pirwww/dbinfo/iproclass.shtml
Web client for visualizing protein sequence feature information using DAS. Provide a highly integrated visualization of protein features; works by accession numbers.
http://www.ebi.ac.uk/dasty/
Prediction Of Unknown Sub-types (PROUST) II. Given a protein sequence alignment, and a classification of some or all of the sequences in the same alignment into functional or other sub-types, PROUST-II predicts positions in the alignment and particular amino acids in them that confer the specific types.
http://www.russell.embl.de/proust2/
The ELM Server is a resource for predicting functional sites (described by the Eukaryotic Linear Motif database) in eukaryotic proteins.
http://elm.eu.org/
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
http://www.pantherdb.org/
Browse the PANTHER system using the Prowler, and retrieve results for different data associated with the ontology and pathway terms, such as individual genes or families and subfamilies of proteins.
http://www.pantherdb.org/panther/prowler.jsp?checkJavaVersion=0
SMAT (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures
http://smart.embl-heidelberg.de/