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SWISS-PROT + TrEMBL
The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database, which are not yet integrated into SWISS-PROT.

Quaternary Structure Prediction
An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design.

Proteomics Analysis: Z3 and LabOnWeb's Z3OnWeb
Proteomic analysis for analyzing 2D-Gel images. Use Compugen's Z3 or Z3OnWeb utitlities for automatic spot detection and registration (=alignment) of protein gel images to match the spots.

The Protein Information Resource
In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a comprehensive, annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.

InterPro - The Integrated Resource of Protein Domains and Functional Sites.
A database built from Pfam, PRINTS and PROSITE.

Combinatorial Extension of Polypeptides
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.

Munich Information Center for Protein Sequences (MIPS)
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.

Entelechon Backtranslation tool
Online backtranslation tool for translating a protein sequence into a DNA sequence. The codon usage can be downloaded from a database and adjusted manually for each amino acid, if required. Java applet.

Protonet
Provides automatic hierarchical classification of proteins sequences.

PredictProtein Server
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.