NOTE: Due to the integration of Swiss-Prot into UniProt (Universal Protein Resource), which is financially supported by a grant from the U.S. National Institute of Health, the usage of Swiss-Prot by both commercial entities and for-profit organizations no longer requires the payment of any license fees.

Protein Databases

Researchers require an ever-increasing amount of in-depth and up-to-date information. To satisfy this thirst for high quality data, GeneBio has since 1998 provided access to SIB Swiss Institute of Bioinformatics' comprehensive annotated proteomics databases: Swiss-Prot, PROSITE and SWISS-2DPAGE. These state-of-the-art databases provide the information needed towards research optimization.

GeneBio and SIB continue to collaborate in order to deliver to the scientific community high quality databases covering different fields of application. In this respect, GeneBio and SIB have added SwissSideChain and SwissBioisostere on their catalogue in order to further enhance drug discovery.


Swiss-Prot, the manually curated section of the UniProt Knowledgebase, was created by Amos Bairoch in 1986 and quickly became such a reference that every life scientist dealing with proteomics needed to access it. Today, Swiss-Prot is known throughout the world as the gold standard for protein research.

The Swiss-Prot knowledgebase does more than just collect information on protein sequences. It is an extensively cross-linked database that connects the various findings in the diverse field of proteomics research. In addition to the core sequence data, references and taxonomy, every Swiss-Prot entry includes manually annotated information (such as function, structure, variants, PTMs, tissue specificity, features, etc.). Swiss-Prot also merges sequence data to minimize redundancy and is cross-referenced with a variety of different databases and bioinformatics tools.

The Geneva Swiss-Prot group develops and improves the UniProtKB/Swiss-Prot protein knowledgebase, the most widely used protein information resource. This activity is carried out in close collaboration with the Hinxton EMBL outstation, the European Bioinformatics Institute (EBI). Its goal is to provide the worldwide Life Science community with the highest quality level of protein-related information. Since 2003, in the framework of the Universal Protein Resource (UniProt) project, such a collaborative endeavor also encompasses the PIR (Protein Information Resource) group from the Georgetown University Medical Center, Washington DC.


PROSITE is a database of protein families and domains. It is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. PROSITE is comprised of the specific signatures for over a thousand protein families or domains. Information on the structure and function of these proteins as well as the consensus pattern for the signature and a list of references are provided.


SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2D PAGE) and SDS-PAGE database established in 1993 and maintained collaboratively by the Biomedical Proteomics Research Group (BPRG) of the Geneva University Hospital and the SIB Swiss Institute of Bioinformatics. Besides the 2D PAGE images showing the determined location of the protein, as well as a theoretical region computed from the protein sequence, the database provides textual data on each protein (including mapping procedures, physiological and pathological information, experimental data and bibliographical references) as well as cross-references to Medline, other federated 2-D databases and to Swiss-Prot.


SwissSideChain is a structural and molecular mechanics database of hundreds of non-natural amino-acid side chains that can be used to study in silico their insertion into natural peptides or proteins.

Amino acids form the building blocks of all proteins and peptides. Natural amino acids are restricted to a few tens of side chains, even when considering post-translation modifications. Nevertheless, the potential chemical diversity of side chains is nearly infinite. Exploiting this diversity by using non-natural side chains has found widespread applications in peptide synthesis and peptidomimetics drug design very recently. SwissSideChain was developed to provide a central platform for researchers working in peptide synthesis, drug design, computational Biology and computational Chemistry, and aiming at using non natural side chains.

In SwissSideChain, a large amount of curated data for hundreds of commercially available non-natural amino acid side chains both in L- and D-form was generated or collected. This includes descriptions of physico-chemical properties, rotamers, information about providers, links to PubChem and other databases, online visualization of the 2D and 3D structures, plugins for inserting non-natural side chains into crystal structures, as well as data files enabling researchers to use non-natural side chains in molecular modeling software.


The SwissBioisostere database provides information on more than 5.6 million molecular sub-structural replacements that have been extracted from literature, along with their performance in biochemical assays.

It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, as well as to give interested scientists access to the details on particular molecular replacements. The accessible data were created through detection of matched molecular pairs and mining bioactivity data in the ChEMBL database, covering more than 35000 assays against 1948 targets representing 30 target classes.

GeneBio recommends access to these databases through the ExPASy server or an ExPASy mirror site as these sites are maintained by SIB Swiss Institute of Bioinformatics. The ExPASy sites provide the latest 'updates' and 'releases' of the PROSITE and SWISS-2DPAGE databases. ExPASy also offers cutting edge proteomic tools and software packages.

SwissSideChain can be accessed through the web site Data contained in SwissSideChain can be accessed and visualized online or downloaded for local usage. The plugins allowing visualization and amino-acid insertion into proteins and peptides using the graphical user interface of UCSF chimera and PyMol can be downloaded from the same location.

SwissBioisostere can be accessed through the web site Data contained in SwissBioisostere can only be accessed and visualized online.

PROSITE, SWISS-2DPAGE, SwissSideChain and SwissBioisostere are developed and copyrighted by SIB Swiss Institute of Bioinformatics.

Access to these databases by commercial entities is subject to the licensing conditions outlined in the User Notice (PDF) and the SIB License (PDF). Please contact us for further details. Please read the SIB Database Legal Disclaimer.