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Expasy

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 genomics, proteomics, systems biology, and clinical applications.^[1] 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.^[1] 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.^[1] Freely available under a Creative Commons 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 SWISS-MODEL for protein structure prediction.^[1]^[2]^[3] Its pioneering role has made it a cornerstone of bioinformatics, emphasizing user-centric design and open access to foster innovation in biomedical research.^[1]

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).^[1] Originally launched in 1993 as the Expert Protein Analysis System (ExPASy), it has evolved into a central hub for life sciences research.^[1] The primary purpose of Expasy is to provide free, open-access resources to support researchers in fields such as genomics, proteomics, and related areas of life sciences and biomedicine.^[1] 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.^[1]^[4] 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.^[3]^[5] It stands as one of the earliest web-based servers for life science applications, having pioneered online access to such resources since its inception.^[1]

Scope and Domains

Expasy encompasses a broad spectrum of biological and computational domains within bioinformatics, primarily focusing on proteomics, which includes the analysis of protein sequences and structures; genomics, encompassing gene expression patterns and viral genomics pipelines; metabolomics; structural biology; systems biology; transcriptomics; glycomics; metagenomics; medicinal chemistry; evolution and phylogeny; and population genetics.^[5]^[3] These areas provide foundational support for understanding molecular mechanisms in living organisms, from sequence-level details to higher-order biological networks.^[1] The portal emphasizes interdisciplinary applications, facilitating advancements in life sciences through integrated data analysis, clinical research by enabling biomarker identification and disease modeling, and drug design via predictive modeling of molecular interactions.^[5] Recent enhancements as of May 2025 include ExpasyGPT, a generative AI tool integrated into the portal to improve biological discovery using knowledge representation across SIB resources.^[6] This holistic approach bridges computational tools with experimental biology, promoting discoveries in areas such as personalized medicine and evolutionary studies.^[1] 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.^[5] All resources are freely accessible under the Creative Commons Attribution 4.0 (CC BY 4.0) license, supporting global research without barriers.^[1] This progression reflects the growing complexity of biological data and the need for unified platforms in modern research.^[5]

History

Founding and Early Years

Expasy was founded in August 1993 by Ron Appel and Amos Bairoch at the University of Geneva in Switzerland.^[1]^[7] 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.^[1]^[8] Created at the dawn of the internet 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 biological data.^[1]^[9] Its development responded to the pressing need for accessible bioinformatics resources during the early genomics boom. The platform's early focus centered on protein analysis tools and databases, enabling researchers to perform tasks such as sequence alignment, motif identification, and structure prediction through a user-friendly interface.^[1]^[7] This foundational work laid the groundwork for collaborative bioinformatics efforts in Switzerland, contributing to the establishment of the Swiss Institute of Bioinformatics (SIB) in 1998, which later integrated and expanded ExPASy's capabilities.^[9]

Key Milestones and Evolution

Following the founding of Expasy in 1993 by Ron Appel and Amos Bairoch as a server for life science information, a key milestone occurred in 1998 with its integration into the newly established Swiss Institute of Bioinformatics (SIB).^[9]^[10] This integration aligned Expasy with SIB's mission to coordinate and foster bioinformatics excellence in Switzerland, marking the portal's transition from an independent resource to a central component of a national institute.^[11] In 2011, Expasy underwent a significant rebranding to become the SIB Expasy Bioinformatics Resources Portal, reflecting the broadening scope of bioinformatics activities under SIB since its inception.^[12]^[13] 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.^[5] 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, interoperability, and overall user experience.^[1]^[14] This version emphasized responsive design and seamless integration of SIB resources, addressing feedback on navigation and accessibility to better serve the global scientific community.^[13] Ongoing annual updates include enhancements to tool integrations, interface usability, and performance optimizations, with recent examples in 2025 such as the PROSITE release 2025_04.^[15] These iterative developments ensure the portal remains adaptable to advancing bioinformatics needs. Expasy's evolution has been highlighted in scientific literature, notably in a 2021 Nucleic Acids Research publication detailing its user-centered design and resource integration (DOI: 10.1093/nar/gkab225).^[13]

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.^[1]^[9] This affiliation began following SIB's formation in 1998, integrating Expasy into a structured framework for advancing computational biology in Switzerland.^[9] 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.^[1] These groups contribute specialized expertise, ensuring that resources remain up-to-date, interoperable, and aligned with evolving scientific needs in proteomics, genomics, and related fields.^[16] 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.^[17] 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 data analysis, storage, and interpretation in the life sciences.^[16]^[1] This alignment promotes FAIR (Findable, Accessible, Interoperable, Reusable) principles, fostering collaboration and innovation across disciplines.^[16]

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.^[1] 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.^[18]^[19] 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 Creative Commons Attribution (CC BY 4.0) license, with ongoing maintenance integrated into SIB's infrastructure, including investments in personnel and lean administrative support.^[16]^[1] Governance is provided by SIB's executive management, including the Directors’ Office and Board of Directors, which validate strategies and allocate funds, supplemented by input from an international Scientific Advisory Board of renowned experts.^[20] Sustainability is achieved through a combination of stable SERI grants, competitive funding from European projects and industry partnerships totaling about 31% of SIB's income as of 2024, and strategic reserves, enabling Expasy to meet growing demands in bioinformatics resource provision.^[19]^[18] Additionally, annual contributions to the Nucleic Acids Research database issue enhance visibility and garner further support by highlighting Expasy's resources and updates, as demonstrated in recent publications.^[1]^[13]

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.^[21] 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.^[22] ENZYME 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.^[23] SwissLipids serves as a curated knowledgebase for lipid structures and metabolism, integrating mass spectrometry identifications with pathways and integrating data from sources like LIPID MAPS to support lipidomics research.^[24] 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.^[25] For genomics, Metabolomics resources on Expasy include integrations with the Human Metabolome Database (HMDB), which provides detailed metabolite profiles, pathways, and spectral data, linked through tools for cross-referencing human metabolic information.^[26] In structural biology, databases connect to Protein Data Bank (PDB) entries via resources like the SWISS-MODEL Repository, which stores homology models of protein structures to complement experimentally determined PDB data.^[27] 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 ENZYME or structural models in SWISS-MODEL—for comprehensive biological analyses.^[2] All are searchable through the Expasy portal's unified interface, supporting queries by keywords, sequences, or identifiers.^[3] Expert curation ensures high standards, with contributions from domain specialists to annotate and validate content.^[28] Updates occur regularly to reflect new research; for instance, UniProtKB releases occur approximately quarterly, incorporating fresh annotations and sequence data.^[29]

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.^[3] These tools are primarily web-based for user accessibility, with many available as open-source software, enabling researchers to perform computations without local installation.^[21] 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.^[30] 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.^[31] Alignment tools like SIM further support this category by identifying optimal non-intersecting alignments between protein sequences.^[32] For structure prediction, SWISS-MODEL 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.^[33] This tool facilitates accessible protein modeling for life scientists by leveraging comparative methods without requiring advanced expertise.^[34] Drug design tools on Expasy include the SwissDrugDesign suite, which encompasses applications for molecular docking, pharmacokinetics prediction, and virtual screening; for instance, SwissDock performs protein-ligand docking simulations to identify potential binding poses.^[35] SwissTargetPrediction complements this by forecasting targets for small molecules in human and vertebrate proteomes, aiding in lead optimization.^[36] 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.^[37] Additional simulation software, such as SimuCell3D, enables 3D modeling of tissue growth and cellular interactions at subcellular resolution.^[38] These tools are predominantly developed by SIB research groups, ensuring alignment with high-quality bioinformatics standards, and many incorporate open-source components for reproducibility and community extension.^[21] Integration with Expasy's databases is a core feature; for example, ProtParam and SWISS-MODEL directly query UniProtKB for sequence inputs and output links to related entries, streamlining workflows from data retrieval to analysis.^[30]^[33]

Portal Features

Search Functionality

The Expasy portal features a central search engine 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.^[14]^[13] For instance, entering a term like "virus" in the search bar retrieves relevant results displayed as interactive cards, enabling quick access to matching entries.^[13] To refine queries, the interface includes a filter panel on the left side, permitting users to narrow results by category (e.g., databases or tools), type, or scientific domain such as proteomics or genomics.^[13] Results are ranked primarily by relevance, prioritizing the most pertinent resources based on keyword matching and contextual alignment.^[13] While advanced operators like Boolean logic are supported in individual resource searches (e.g., within UniProt), the portal's core search emphasizes straightforward keyword-based discovery without explicit site-specific constraints.^[39] Resource discovery extends beyond direct searches through categorized browsing, where users can navigate hubs organized by domains like proteomics or transcriptomics to explore related tools and databases systematically.^[3] Key resources, such as UniProt 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.^[13] In May 2025, Expasy introduced ExpasyGPT, an AI-powered feature that enables natural language queries to retrieve and compile information from the portal's resources, further enhancing discovery capabilities.^[6] These enhancements were introduced in the Expasy 3.0 redesign launched in 2020, improving search speed, mobile responsiveness, and overall user navigation.^[14]

User Access and Interface

The Expasy portal features a modern web design introduced in version 3.0, launched in October 2020, which emphasizes user-centered design principles derived from extensive user studies to enhance accessibility and usability. 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.^[1]^[40] Access to Expasy resources is entirely free and open to the global scientific community, licensed under Creative Commons 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 API endpoints, enabling automated queries and data retrieval without manual intervention through the web interface—for instance, the Translate tool supports POST requests for sequence translation. This open-access model facilitates seamless incorporation into research workflows, from basic sequence analysis 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 documentation 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 SWISS-MODEL. 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 personal data 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 research.^[41]

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.^[42] 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.^[13] This growth was further accelerated by the integration of COVID-19-specific genomics tools, such as V-pipe, a pipeline for analyzing SARS-CoV-2 sequencing data that saw heightened use during the pandemic.^[43]^[44] The portal's global reach encompasses a broad user base. These patterns are monitored through standard web analytics tools to inform ongoing enhancements.^[42] 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.^[13] Expasy operates on a free access model, enabling unrestricted use by the international scientific community.^[3]

Scientific Contributions

Expasy has significantly advanced protein annotation through its hosting of UniProt, a comprehensive resource that provides accurate sequence data and functional information for millions of proteins, enabling breakthroughs in understanding protein roles in biological processes.^[45] UniProt's automated and manual annotation pipelines have facilitated large-scale functional predictions, supporting research in genomics and proteomics by standardizing protein knowledge across species.^[45] This resource has been instrumental in identifying novel protein functions and interactions, contributing to foundational work in molecular biology. In protein structure prediction, Expasy's SWISS-MODEL tool has played a key role by providing homology modeling capabilities that complement and validate predictions from advanced methods like AlphaFold.^[46] SWISS-MODEL 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 drug design and functional studies.^[47] These contributions have enhanced the accuracy of structural biology 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 COVID-19 outbreak, by processing next-generation sequencing data to detect variants and assess genetic diversity in SARS-CoV-2 samples.^[43] Adapted specifically for SARS-CoV-2, V-pipe supports reproducible variant calling and haplotype reconstruction, informing epidemiological tracking and therapeutic development in real-time outbreak scenarios.^[48] Its application in large-scale studies has advanced understanding of viral evolution and resistance mechanisms. Expasy's resources receive annual recognition in the Nucleic Acids Research database issue, highlighting their reliability and integration in bioinformatics workflows.^[13] 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.^[5] 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.^[6] UniProt and related resources are highly cited in scientific papers, underscoring their high-impact role in advancing biomedical research.^[49]

References

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The Scientific Advisory Board acts as an independent consultative body, providing recommendations to the Board of Directors and the Executive Management.
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Over 160 tools and databases are developed by the SIB community and openly available on Expasy, the Swiss Bioinformatics Resource Portal.
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The UniProt Knowledgebase is a central hub for the collection of functional information on proteins with accurate, consistent and rich annotation.
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Translate is a tool which allows the translation of a nucleotide (DNA/RNA) sequence to a protein sequence. DNA or RNA sequence. Output format.
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### Summary of Data Privacy Compliance (GDPR for Expasy/SIB Resources)
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