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Expasy is an online bioinformatics resource operated by the SIB Swiss Institute of Bioinformatics. It is an extensible and integrative portal which provides access to over 160 databases and software tools and supports a range of life science and clinical research areas, from genomics, proteomics and structural biology, to evolution and phylogeny, systems biology and medical chemistry. The individual resources (databases, web-based and downloadable software tools) are hosted in a decentralized way by different groups of the SIB Swiss Institute of Bioinformatics and partner institutions.

Search engine

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Queries of Expasy allow:

  1. parallel searches SIB databases through a single search
  2. aggregated search results from the complete set of >160 resources accessible from the portal.[1]

Expasy provides up-to-date information from the most recent release of each resources.

The terms used in Expasy are based on the EDAM comprehensive ontology.[2]

History

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Expasy was created in August 1993. Originally, it was called ExPASy (Expert Protein Analysis System) and acted as a proteomics server to analyze protein sequences and structures and two-dimensional gel electrophoresis (2-D Page electrophoresis).[3] Among others, ExPASy hosted the protein sequence knowledge base, UniProtKB/Swiss-Prot, and its computer annotated supplement, UniProtKB/TrEMBL.[4]

ExPASy was the first website of the life sciences and among the first 150 websites in the world. As of 5 April 2007, ExPASy had been consulted 1 billion times since its installation on 1 August 1993.[5]

In June 2011, it became the SIB ExPASy Bioinformatics Resources Portal: a diverse catalogue of bioinformatics resources developed by SIB Groups.[6] The current version of Expasy was released in October 2020.[7][8]

Notes and references

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Expasy

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Expasy is the bioinformatics resource portal of the SIB Swiss Institute of Bioinformatics, serving as a comprehensive registry of software tools, databases, and datasets developed by SIB for advancing research in life sciences, including , , , and clinical applications. Originally launched in August 1993 as ExPASy (Expert Protein Analysis System) by Ron Appel and Amos Bairoch, it was one of the first websites dedicated to life sciences and among the earliest 150 websites globally, initially focused on protein analysis but evolving into a broader, extensible platform. In June 2011, it was rebranded as the SIB Expasy Bioinformatics Resources Portal, and its current version, Expasy 3.0, was released in October 2020 following extensive user studies to enhance accessibility and integration. Freely available under a Attribution (CC BY 4.0) license and funded by the Swiss State Secretariat for Education, Research and Innovation (SERI), Expasy supports a global community of researchers by providing 134 resources (as of November 2025), such as UniProtKB/Swiss-Prot for protein annotations and tools like for . Its pioneering role has made it a cornerstone of bioinformatics, emphasizing user-centric design and to foster innovation in biomedical research.

Overview

Definition and Purpose

Expasy is the SIB Bioinformatics Resource Portal, serving as a comprehensive registry for bioinformatics software tools, databases, knowledgebases, and datasets primarily developed by members of the Swiss Institute of Bioinformatics (SIB). Originally launched in 1993 as the Expert Protein Analysis System (ExPASy), it has evolved into a central hub for life sciences research. The primary purpose of Expasy is to provide free, open-access resources to support researchers in fields such as , , and related areas of life sciences and . All content is made available under the Creative Commons Attribution 4.0 International (CC BY 4.0) license, ensuring broad accessibility and reusability for the global scientific community. As an extensible and integrative platform, Expasy aggregates over 160 high-quality resources developed mainly by SIB groups, facilitating discovery and utilization of bioinformatics tools and data. It stands as one of the earliest web-based servers for life science applications, having pioneered access to such resources since its inception.

Scope and Domains

Expasy encompasses a broad spectrum of biological and computational domains within bioinformatics, primarily focusing on , which includes the analysis of protein sequences and structures; , encompassing gene expression patterns and viral genomics pipelines; ; ; ; transcriptomics; glycomics; ; ; and phylogeny; and . These areas provide foundational support for understanding molecular mechanisms in living organisms, from sequence-level details to higher-order biological networks. The portal emphasizes interdisciplinary applications, facilitating advancements in life sciences through integrated , by enabling identification and disease modeling, and via predictive modeling of molecular interactions. Recent enhancements as of May 2025 include ExpasyGPT, a generative AI tool integrated into the portal to improve biological discovery using representation across SIB resources. This holistic approach bridges computational tools with experimental , promoting discoveries in areas such as and evolutionary studies. Expasy integrates high-quality, curated resources developed by the SIB Swiss Institute of Bioinformatics alongside contributions from select external institutions, ensuring reliability and standardization across datasets. All resources are freely accessible under the Creative Commons Attribution 4.0 (CC BY 4.0) license, supporting global research without barriers. This progression reflects the growing complexity of biological data and the need for unified platforms in modern research.

History

Founding and Early Years

Expasy was founded in August 1993 by Ron Appel and Amos Bairoch at the in . Initially named ExPASy, standing for Expert Protein Analysis System, it emerged as a pioneering initiative to provide computational tools for protein research amid the burgeoning field of bioinformatics. Created at the dawn of the era, ExPASy was one of the first web servers dedicated to life sciences, ranking among the world's initial 150 websites and facilitating early online access to . Its development responded to the pressing need for accessible bioinformatics resources during the early boom. The platform's early focus centered on protein analysis tools and databases, enabling researchers to perform tasks such as , motif identification, and structure prediction through a user-friendly interface. This foundational work laid the groundwork for collaborative bioinformatics efforts in , contributing to the establishment of the Swiss Institute of Bioinformatics (SIB) in , which later integrated and expanded ExPASy's capabilities.

Key Milestones and Evolution

Following the founding of Expasy in 1993 by Ron Appel and Amos Bairoch as a server for , a key milestone occurred in with its integration into the newly established Swiss Institute of Bioinformatics (SIB). This integration aligned Expasy with SIB's mission to coordinate and foster bioinformatics excellence in , marking the portal's transition from an independent resource to a central component of a national institute. In 2011, Expasy underwent a significant to become the SIB Expasy Bioinformatics Resources Portal, reflecting the broadening scope of bioinformatics activities under SIB since its . This update expanded the portal beyond its initial focus on protein-related tools to encompass integrative resources across various life sciences, enhancing its role as a comprehensive entry point for SIB-maintained databases and software. The release of Expasy 3.0 in October 2020 represented another major evolution, introducing a modern web architecture designed after extensive user studies to improve extensibility, , and overall . This version emphasized responsive design and seamless integration of SIB resources, addressing feedback on navigation and accessibility to better serve the global scientific community. Ongoing annual updates include enhancements to tool integrations, interface usability, and performance optimizations, with recent examples in 2025 such as the release 2025_04. These iterative developments ensure the portal remains adaptable to advancing bioinformatics needs. Expasy's evolution has been highlighted in , notably in a 2021 publication detailing its and resource integration (DOI: 10.1093/nar/gkab225).

Organization and Management

Affiliation with SIB

Expasy has been hosted and managed by the Swiss Institute of Bioinformatics (SIB) since 1998, serving as the organization's official portal for bioinformatics resources. This affiliation began following SIB's formation in 1998, integrating Expasy into a structured framework for advancing in . SIB plays a central role in the development, curation, and maintenance of the majority of Expasy's databases and tools, primarily through its member research groups distributed across Swiss institutions. These groups contribute specialized expertise, ensuring that resources remain up-to-date, interoperable, and aligned with evolving scientific needs in , , and related fields. For user support, SIB operates the Expasy helpdesk, handling general technical queries and issue resolution through dedicated contact forms on the portal, while resource-specific support is available for submissions and updates to individual databases and tools. This service facilitates seamless interaction between the global research community and SIB's bioinformatics infrastructure. Expasy's integration with SIB's broader mission enhances bioinformatics research both nationally and internationally by providing centralized access to high-quality, curated tools that support , storage, and interpretation in the life sciences. This alignment promotes (Findable, Accessible, Interoperable, Reusable) principles, fostering collaboration and innovation across disciplines.

Funding and Operations

Expasy receives its primary funding from the Swiss State Secretariat for Education, Research and Innovation (SERI), which provides the core financial support for its development and maintenance as part of the SIB Swiss Institute of Bioinformatics. In January 2025, the Swiss Confederation renewed this core funding for the 2025-2028 period at the previous level of CHF 46.5 million total, covering approximately 48% of SIB's annual budget as of the 2025-2028 period, with a significant portion—around 57% of the SERI allocation as of 2024—dedicated to sustaining open bioinformatics resources like those hosted on Expasy. As a non-profit initiative under SIB, Expasy operates on a model that ensures all resources are freely accessible to the global scientific community under a Attribution (CC BY 4.0) license, with ongoing maintenance integrated into SIB's infrastructure, including investments in personnel and lean administrative support. Governance is provided by SIB's executive management, including the Directors’ Office and , which validate strategies and allocate funds, supplemented by input from an international Scientific Advisory Board of renowned experts. Sustainability is achieved through a combination of stable SERI grants, competitive funding from European projects and industry partnerships totaling about 31% of SIB's as of 2024, and strategic reserves, enabling Expasy to meet growing demands in bioinformatics resource provision. Additionally, annual contributions to the database issue enhance visibility and garner further support by highlighting Expasy's resources and updates, as demonstrated in recent publications.

Resources

Databases

Expasy hosts numerous high-quality bioinformatics databases developed by the SIB Swiss Institute of Bioinformatics, serving as central repositories for biological data across various domains. These databases emphasize expert curation to ensure accuracy and reliability, enabling researchers to access validated information on proteins, enzymes, lipids, and other biomolecules. Among the core databases, UniProtKB stands as the primary protein knowledgebase, providing comprehensive functional annotations for millions of protein sequences, including details on structure, interactions, and biological roles, with its Swiss-Prot subset featuring manually curated entries. offers a standardized nomenclature for enzymes, cataloging 6,919 entries (as of October 2025) based on recommendations from the International Union of Biochemistry and Molecular Biology, facilitating classification and retrieval of enzymatic data. SwissLipids serves as a curated knowledgebase for structures and , integrating identifications with pathways and integrating data from sources like LIPID MAPS to support research. In proteomics, neXtProt focuses on human proteins, delivering expert-curated insights into functions, disease associations, and proteomics-derived evidence for approximately 20,000 protein-coding genes. For genomics, Metabolomics resources on Expasy include integrations with the (HMDB), which provides detailed metabolite profiles, pathways, and spectral data, linked through tools for cross-referencing human metabolic information. In structural biology, databases connect to (PDB) entries via resources like the Repository, which stores homology models of protein structures to complement experimentally determined PDB data. These databases are designed for seamless integration, featuring interlinked entries that allow navigation between related data—such as protein sequences in UniProtKB connecting to enzyme classifications in or structural models in —for comprehensive biological analyses. All are searchable through the Expasy portal's unified interface, supporting queries by keywords, sequences, or identifiers. Expert curation ensures high standards, with contributions from domain specialists to annotate and validate content. Updates occur regularly to reflect new research; for instance, UniProtKB releases occur approximately quarterly, incorporating fresh annotations and sequence data.

Software Tools

Expasy provides a comprehensive suite of numerous software tools developed by the SIB Swiss Institute of Bioinformatics, focusing on bioinformatics analysis across various life science domains. These tools are primarily web-based for user accessibility, with many available as open-source software, enabling researchers to perform computations without local installation. In sequence analysis, Expasy offers tools for processing protein and nucleotide sequences, such as ProtParam, which computes physicochemical parameters like molecular weight, theoretical isoelectric point, and amino acid composition from a UniProtKB entry or user-provided sequence. Another example is Translate, a utility for converting DNA or RNA sequences into corresponding protein sequences using standard genetic codes, developed by the Swiss-Prot group. Alignment tools like SIM further support this category by identifying optimal non-intersecting alignments between protein sequences. For structure , stands out as a fully automated homology-modeling server that generates 3D protein models based on template structures, processing millions of requests annually and integrating quality assessment metrics. This tool facilitates accessible protein modeling for life scientists by leveraging comparative methods without requiring advanced expertise. tools on Expasy include the SwissDrugDesign suite, which encompasses applications for molecular docking, pharmacokinetics , and ; for instance, SwissDock performs protein-ligand docking simulations to identify potential binding poses. SwissTargetPrediction complements this by forecasting targets for small molecules in human and vertebrate proteomes, aiding in lead optimization. Systems biology simulations are supported through tools like V-pipe, a pipeline for analyzing next-generation sequencing data to assess viral genetic diversity, haplotype reconstruction, and evolutionary dynamics, particularly useful in pathogen genomics. Additional simulation software, such as SimuCell3D, enables of tissue growth and cellular interactions at subcellular resolution. These tools are predominantly developed by SIB groups, ensuring alignment with high-quality bioinformatics standards, and many incorporate open-source components for reproducibility and community extension. Integration with Expasy's databases is a core feature; for example, ProtParam and directly query UniProtKB for sequence inputs and output links to related entries, streamlining workflows from data retrieval to analysis.

Portal Features

Search Functionality

The Expasy portal features a central that allows users to query across more than 160 bioinformatics resources, including databases and software tools, using keywords related to resource names, descriptions, categories, or specific terms. For instance, entering a term like "" in the search bar retrieves relevant results displayed as interactive cards, enabling quick access to matching entries. To refine queries, the interface includes a filter panel on the left side, permitting users to narrow results by category (e.g., or ), type, or scientific domain such as or . Results are ranked primarily by , prioritizing the most pertinent resources based on keyword matching and contextual alignment. While advanced operators like logic are supported in individual resource searches (e.g., within ), the portal's core search emphasizes straightforward keyword-based discovery without explicit site-specific constraints. Resource discovery extends beyond direct searches through categorized browsing, where users can navigate hubs organized by domains like or transcriptomics to explore related tools and databases systematically. Key resources, such as for protein sequence and annotation data, are prominently highlighted on the homepage and in search results to direct users toward widely used, high-impact entries. In May 2025, Expasy introduced ExpasyGPT, an AI-powered feature that enables queries to retrieve and compile information from the portal's resources, further enhancing discovery capabilities. These enhancements were introduced in the Expasy 3.0 redesign launched in , improving search speed, mobile responsiveness, and overall user navigation.

User Access and Interface

The Expasy portal features a modern introduced in version 3.0, launched in October 2020, which emphasizes principles derived from extensive user studies to enhance and . This version incorporates a responsive layout that adapts seamlessly to various devices, including desktops, tablets, and mobiles, ensuring optimal viewing and interaction regardless of screen size. Navigation is intuitive, with streamlined menus that categorize resources into databases, software tools, and educational materials, allowing users to quickly locate relevant bioinformatics services. Access to Expasy resources is entirely free and open to the global scientific community, licensed under Attribution (CC BY 4.0), with no registration required for the majority of tools and databases to promote broad usage. For advanced programmatic integration, many individual tools offer endpoints, enabling automated queries and data retrieval without manual intervention through the web interface—for instance, the Translate tool supports requests for . This open-access model facilitates seamless incorporation into research workflows, from basic to complex proteomic studies. User support is robust, featuring a dedicated Expasy Helpdesk for handling submissions, technical issues, and general inquiries via a contact form on the portal. Comprehensive pages detail resource functionalities, usage guidelines, and best practices, while tutorials—often in video or step-by-step formats—are available for key tools to guide users through processes like protein modeling with . These resources ensure that researchers, regardless of expertise level, can effectively utilize the platform. Technically, Expasy is hosted on secure servers managed by the SIB Swiss Institute of Bioinformatics, leveraging Switzerland's robust data protection framework. The infrastructure complies with the General Data Protection Regulation (GDPR) for applicable processing activities, such as user support interactions, safeguarding like email addresses collected via forms. While specific uptime metrics are not publicly detailed, SIB's commitment to reliable service supports continuous availability for critical life sciences .

Impact and Recognition

Usage and Adoption

Expasy receives millions of annual visits from academic and industry researchers worldwide. Web analytics indicate hundreds of thousands of monthly visits as of October 2025, reflecting sustained high traffic primarily from life sciences professionals. Adoption has shown notable trends since 2020, driven by the launch of Expasy 3.0, which increased daily users by 15% through improved usability and responsive design. This growth was further accelerated by the integration of COVID-19-specific tools, such as V-pipe, a pipeline for analyzing sequencing data that saw heightened use during the . The portal's global reach encompasses a broad user base. These patterns are monitored through standard tools to inform ongoing enhancements. Community engagement is fostered via opportunities for external users to submit and contribute to resources, alongside extensive citations of Expasy-hosted databases and tools in peer-reviewed publications. Expasy operates on a free access model, enabling unrestricted use by the international .

Scientific Contributions

Expasy has significantly advanced protein through its hosting of , a comprehensive resource that provides accurate sequence data and functional information for millions of proteins, enabling breakthroughs in understanding protein roles in biological processes. 's automated and manual annotation pipelines have facilitated large-scale functional predictions, supporting research in and by standardizing protein knowledge across . This resource has been instrumental in identifying novel protein functions and interactions, contributing to foundational work in . In , Expasy's tool has played a key role by providing capabilities that complement and validate predictions from advanced methods like . integrates AlphaFold-derived structures as templates and employs quality assessment metrics such as QMEANDisCo and predicted local Distance Difference Test (pLDDT) to evaluate model reliability, aiding researchers in refining structural hypotheses for and functional studies. These contributions have enhanced the accuracy of research, particularly in validating AI-generated models against experimental data. For viral genomics, Expasy's V-pipe pipeline has enabled critical analyses during pandemics, including the outbreak, by processing next-generation sequencing data to detect variants and assess genetic diversity in samples. Adapted specifically for , V-pipe supports reproducible variant calling and haplotype reconstruction, informing epidemiological tracking and therapeutic development in real-time outbreak scenarios. Its application in large-scale studies has advanced understanding of and resistance mechanisms. Expasy's resources receive annual recognition in the Nucleic Acids Research database issue, highlighting their reliability and integration in bioinformatics workflows. These tools have influenced standards for data sharing by promoting interoperable formats and open-access principles, fostering collaborative research in personalized medicine and drug discovery. As of 2025, Expasy continues to drive AI-driven biology through initiatives like ExpasyGPT, which enhances multi-omics integration by querying interconnected databases for insights into complex biological systems. UniProt and related resources are highly cited in scientific papers, underscoring their high-impact role in advancing biomedical research.

References

  1. https://www.expasy.org/about
  2. https://www.expasy.org/resources/uniprotkb-swiss-prot
  3. https://www.expasy.org/
  4. https://creativecommons.org/licenses/by/4.0/
  5. https://pmc.ncbi.nlm.nih.gov/articles/PMC8265094/
  6. https://www.sib.swiss/news/expasygpt-enhanced-biological-discovery-with-ai-and-knowledge-representation
  7. https://pubmed.ncbi.nlm.nih.gov/12824418/
  8. https://academic.oup.com/nar/article/31/13/3784/2904185
  9. https://www.sib.swiss/about/who-we-are/history
  10. https://pmc.ncbi.nlm.nih.gov/articles/PMC4086091/
  11. https://www.researchgate.net/publication/262050982_Fifteen_years_SIB_Swiss_Institute_of_Bioinformatics_Life_science_databases_tools_and_support
  12. https://www.eurekalert.org/news-releases/604237
  13. https://academic.oup.com/nar/article/49/W1/W216/6225225
  14. https://www.sib.swiss/news/discover-the-new-expasyorg-the-swiss-bioinformatics-resource-portal
  15. https://prosite.expasy.org/
  16. https://www.sib.swiss/
  17. https://www.expasy.org/contact
  18. https://www.sib.swiss/news/swiss-confederation-renews-sib-funding-for-2025-2028
  19. https://www.sib.swiss/about/funding-sources
  20. https://www.sib.swiss/about/governance-and-organization
  21. https://www.sib.swiss/services/open-software-and-databases
  22. https://www.expasy.org/resources/uniprotkb
  23. https://enzyme.expasy.org/
  24. https://www.expasy.org/resources/swisslipids
  25. https://www.expasy.org/resources/nextprot
  26. https://hmdb.ca/
  27. https://www.expasy.org/resources/swiss-model-repository
  28. https://www.sib.swiss/swiss-prot
  29. https://web.expasy.org/docs/relnotes/relstat.html
  30. https://web.expasy.org/protparam/
  31. https://web.expasy.org/translate/
  32. https://web.expasy.org/sim/
  33. https://swissmodel.expasy.org/
  34. https://www.expasy.org/resources/swiss-model
  35. https://www.expasy.org/resources/swissdrugdesign
  36. https://www.expasy.org/resources/swisstargetprediction
  37. https://www.expasy.org/resources/v-pipe
  38. https://www.expasy.org/resources/simucell3d
  39. https://web.expasy.org/docs/history.html
  40. https://www.researchgate.net/publication/350872619_Expasy_the_Swiss_Bioinformatics_Resource_Portal_as_designed_by_its_users
  41. https://www.sib.swiss/privacy-policy
  42. https://www.similarweb.com/website/expasy.org/
  43. https://www.sib.swiss/news/the-viral-genomics-pipeline-v-pipe-under-the-spotlight
  44. https://www.expasy.org/resources/v-pipe-sars-cov-2
  45. https://academic.oup.com/nar/article/53/D1/D609/7902999
  46. https://swissmodel.expasy.org/docs/references
  47. https://academic.oup.com/nar/article/52/W1/W318/7650609
  48. https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giae065/7795669
  49. https://www.uniprot.org/uniprotkb/statistics
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