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

Harvester collects and displays bioinformatic protein information and predictions for human proteins from various databases for realtime access.

The ELM Server is a resource for predicting functional sites described by the Eukaryotic Linear Motif database in eukaryotic proteins.

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.

ANTHEPROT (ANalyse THE PROTeins) is the result of about 10 years of biocomputing activity of a group of the Institute of Biology and Chemistry of Proteins. The main idea was to integrate into a single package most of the methods designed for protein sequence analysis (1,2,3,4). This simple idea was originally supported early in 1988!

Web client for visualizing protein sequence feature information using DAS. Provide a highly integrated visualization of protein features; works by accession numbers.

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.

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.

SMAT (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures

Inference of protein function from protein structure

The Prolinks database is a collection of inference methods used to predict functional linkages between proteins. These methods include the Phylogenetic profile method which uses the presence and absence of proteins across multiple genomes to detect functional linkages; the Gene Cluster method, which uses genome proximity to predict functional linkage; Rosetta Stone, which uses a gene fusion event in a second organism to infer functional relatedness; and the Gene Neighbor method, which uses both gene proximity and phylogenetic distribution to infer linkage.

Proteome Analyst (PA) is an online tool used by researchers to rapidly analyze proteins. Using machine learning technologies, PA can accurately predict the subcellular localization and high level function of user submitted proteins.

Protein Link Explorer (PLEX). Given an amino acid sequence or its GenBank sequence identifier, PLEX allows a phylogenetic profile to be constructed, which can subsequently be compared to profiles of upto 350,111 other proteins from 89 fully sequenced genomes, that are stored in our database. In addition, PLEX can accept sophisticated phylogenetic profile inputs and comparison parameters, including individual organism or group-based profiles. Gene neighbors and rosetta stone links of all proteins that match the query profile can also be investigated.

JAFA is the Joined Assembly of Function Annotations, a protein function prediction meta-server. JAFA accepts a protein sequence as input, queries several function prediction programs, and produces results assembled from these servers.

Firestar predicts functionally important residues.

FSSA: A novel method for identifying functional signatures from structural alignments.

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.

WebFEATURE allows a user to scan a molecular structure for a particular functional site (e.g. ATP binding site, calcium binding site, etc.).

This web site is a new tool to identify putative Protein Phosphatase 1 (PP1) binding proteins.