SIB develops, supplies and maintains more than 150 high-quality databases and software platforms for the global life science research community. Most of SIB resources are in open-access on ExPASy, the SIB bioinformatics resource portal. The SIB resources cover different areas of life sciences, such as genomics, proteomics and evolution.

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Some examples of our resources are presented below. Please click on the resource name to find out more about the resource and to access the corresponding webpage.

 

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UniProtKB/Swiss-Prot – Protein sequence database
Ioannis Xenarios & Lydie Bougueleret group
UniProtKB/Swiss-Prot is the most widely used protein information resource in the world, with over 900,000 requests per month. It provides concise, but thorough, descriptions of a non-redundant set of hundred thousands of proteins including their function, domain structure, post-translational modifications and variants. Its high-quality annotation is the fruit of manual expert curation by biologists, who use information available in the scientific literature to provide an accurate description of each protein’s features.

 

 

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neXtProt – Human protein knowledge platform
Amos Bairoch & Lydie Lane group
neXtProt is an innovative knowledge platform dedicated to human proteins. neXtProt includes curated information on various aspects of human protein biology such as function, mRNA/protein expression, protein/protein interactions, post-translational modifications and protein variations. Its aim is to help life science researchers in their quest to unravel the complexity of human life processes.

 

 

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SWISS-MODEL – Structure homology-modelling
Torsten Schwede group
SWISS-MODEL is an automated protein structure homology-modelling server for generating 3D models of a protein. Comparative approaches are currently the most accurate and reliable computational methods to derive 3D models of proteins, for which experimental structures are not available. SWISS-MODEL automates the complex process of model building on an easy to use web-based system, thereby making model information also available for non-specialists.

 

 

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STRING – Protein-protein interactions
Christian von Mering group
STRING is a database of known and predicted protein-protein interactions, including direct (physical) and indirect (functional) associations. They are derived from different sources such as the genomic context, high-throughput experiments, (conserved) co-expression, and the literature. STRING quantitatively integrates the interaction data for a large number of organisms, and transfers information between these organisms where applicable. The database currently covers millions of 9,643,763 proteins from a huge number of organisms.

 

 

Swiss Regulon

SwissRegulon – Annotations of regulatory sites
Erik van Nimwegen group
The SwissRegulon web portal provides information and tools for the analysis of genome-wide transcription regulatory networks in organisms ranging from E. coli to human. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.

 

 

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SwissDrugDesign – Drug design
Olivier Michielin & Vincent Zoete group
The SwissDrugDesign project is an ambitious initiative aiming to provide the first comprehensive, integrated and freely accessible web-based in silico drug design environment to the scientific community worldwide. It offers a large collection of tools covering all aspects of computer-aided drug design, from target prediction of small molecules (SwissTargetPrediction) to the provision of topology and parameters of drug-like molecules (SwissParam). Other tools include SwissDock, SwissSideChain and SwissBioisostere.

 

 

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EPD – Collection of eukaryotic promoters
Philipp Bucher group
Genes are first “transcribed” into messenger RNA used as templates to synthesize proteins. Transcription begins on “promoters”. The Eukaryotic Promoter Database (EPD) provides quality-controlled information on experimentally defined promoters of higher organisms as well as web-based tools for promoter analysis.

 

 

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Bgee – Gene expression evolution
Marc Robinson-Rechavi group
Bgee is a database of gene expression evolution, which integrates all types of transcriptome and expression information for animals – including human, model organisms such as mouse or Drosophila, and diverse species of evolutionary or agronomical relevance. Bgee is the only resource which provides homologous expression between species.

 

 

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UniCarbKB – Glycan database
Frédérique Lisacek group
UniCarbKB is a knowledgebase that offers public access to a curated database of information on glycoproteins, which are proteins to which carbohydrates (or glycans) are attached. UniCarbKB provides comprehensive information on glycan structures, and published glycoprotein information including global and site-specific attachment information.

 

 

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SugarBind – Pathogen-sugar binding
Frédérique Lisacek group
Host-pathogen communication is known to be mediated by carbohydrate-protein interactions, which ensure adhesion at cell surface. The SugarBind database covers knowledge of interactions between pathogens and carbohydrate ligands of mammalian hosts. Information in SugarBindDB is manually curated and supports the investigation of microbial or viral infections.

 

 

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OrthoDB – Hierarchical catalogue of orthologs
Gaston Gonnet group
OrthoDB is a catalogue of “equivalent” genes among species, called orthologs. Resolving gene ancestry is the most accurate way to predict putative gene functions by association with genes studied in model organisms. OrthoDB is hence critical both for evolutionary studies and for interpreting gene content from the newly sequenced genomes.

 

 

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OMA – Orthology prediction
Gaston Gonnet group
The Orthology MAtrix (OMA) Browser provides orthology predictions among publicly available genomes. Started in 2004, it has undergone many releases and now elucidates orthology among millions of genes from thousands of species, making it one of the largest resources of its kind.

 

 

2.1 databases table Genes and Genomes Proteins and Proteomes Medicine and Health Evolution and Phytogeny Structural Biology Systems Biology Bioinformatics Infrastructures  
This table shows, for each bioinformatics domain, examples of SIB databases and software that are available on ExPASy.