InterProScan: InterPro is a database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences
Prosite: consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them
The Pfam database is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs)
CATH:The CATH database is a free, publicly available online resource that provides information on the evolutionary relationships of protein domains. It was created in the mid-1990s by Professor Christine Orengo and colleagues, and continues to be developed by the Orengo group at University College London.
SCOP:Structural Classification of Proteins.
SCOP 2: is a successor of Structural classification of proteins (SCOP). Similarly to SCOP, the main focus of SCOP2 is on proteins that are structurally characterized and deposited in the PDB. Proteins are organized according to their structural and evolutionary relationships, but, in contrast to SCOP, instead of a simple tree-like hierarchy these relationships form a complex network of nodes. Each node represents a relationship of a particular type and is exemplified by a region of protein structure and sequence.
SUPERFAMILY:SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
PDBeMotif is an extremely fast and powerful search tool that facilitates exploration of the Protein Data Bank (PDB) by combining protein sequence, chemical structure and 3D data in a single search. Currently it is the only tool that offers this kind of integration at this speed. PDBeMotif can be used to examine the characteristics of the binding sites of single proteins or classes of proteins such as Kinases and the conserved structural features of their immediate environments either within the same specie or across different species.
COFACTOR: structure-based function predictions
CombFunc: Protein Function Prediction Server
The ProFunc server: had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure.
PFQ: Protein Function Prediction
SignalX: Server for predictoin transcription factor binding sites. Search for a common signal in given set of sequences.
COFACTOR: is a structure-based method for biological function annotation of protein molecules.
PredicProtein: Protein Function Prediction Server (*Login Required)
TargetP: predicts the subcellular location of eukaryotic proteins
SLocX: Subcellular Localization using gene eXpression
SignalP 4.1: server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction
list of server for Subcellular Localization Prediction Tools