UniProt ≈ UniProt
View article: UniProt: a worldwide hub of protein knowledge
UniProt: a worldwide hub of protein knowledge Open
The UniProt Knowledgebase is a collection of sequences and annotations for over 120 million proteins across all branches of life. Detailed annotations extracted from the literature by expert curators have been collected for over half a mil…
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Pfam: The protein families database in 2021 Open
The Pfam database is a widely used resource for classifying protein sequences into families and domains. Since Pfam was last described in this journal, over 350 new families have been added in Pfam 33.1 and numerous improvements have been …
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UniProt: the universal protein knowledgebase in 2021 Open
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this article, we describe significant updates that we have…
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The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences Open
The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's largest data repository of mass spectrometry-based proteomics data. PRIDE is one of the founding members of the global ProteomeXchange (PX) conso…
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UniProt: the Universal Protein Knowledgebase in 2023 Open
The aim of the UniProt Knowledgebase is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication we describe enhancements made to our data…
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DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update) Open
DAVID is a popular bioinformatics resource system including a web server and web service for functional annotation and enrichment analyses of gene lists. It consists of a comprehensive knowledgebase and a set of functional analysis tools. …
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UniProt: the universal protein knowledgebase Open
The UniProt knowledgebase is a large resource of protein sequences and associated detailed annotation. The database contains over 60 million sequences, of which over half a million sequences have been curated by experts who critically revi…
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InterPro in 2022 Open
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with …
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dbCAN2: a meta server for automated carbohydrate-active enzyme annotation Open
Complex carbohydrates of plants are the main food sources of animals and microbes, and serve as promising renewable feedstock for biofuel and biomaterial production. Carbohydrate active enzymes (CAZymes) are the most important enzymes for …
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20 years of the SMART protein domain annotation resource Open
SMART (Simple Modular Architecture Research Tool) is a web resource (http://smart.embl.de) for the identification and annotation of protein domains and the analysis of protein domain architectures. SMART version 8 contains manually curated…
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The SWISS-MODEL Repository—new features and functionality Open
SWISS-MODEL Repository (SMR) is a database of annotated 3D protein structure models generated by the automated SWISS-MODEL homology modeling pipeline. It currently holds >400 000 high quality models covering almost 20% of Swiss-Prot/UniPro…
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Database resources of the National Center for Biotechnology Information Open
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstrac…
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InterPro in 2019: improving coverage, classification and access to protein sequence annotations Open
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and i…
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OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs Open
OrthoDB (https://www.orthodb.org) provides evolutionary and functional annotations of orthologs. This update features a major scaling up of the resource coverage, sampling the genomic diversity of 1271 eukaryotes, 6013 prokaryotes and 6488…
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UniProt: the Universal Protein Knowledgebase in 2025 Open
The aim of the UniProt Knowledgebase (UniProtKB; https://www.uniprot.org/) is to provide users with a comprehensive, high-quality and freely accessible set of protein sequences annotated with functional information. In this publication, we…
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DRAM for distilling microbial metabolism to automate the curation of microbiome function Open
Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation softwar…
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RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation Open
The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains nearly 200 000 bacterial and archaeal genomes and 150 million proteins with up-to-date annotation. Changes in the Prokaryotic Geno…
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BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins Open
Interest in secondary metabolites such as RiPPs (ribosomally synthesized and posttranslationally modified peptides) is increasing worldwide. To facilitate the research in this field we have updated our mining web server. BAGEL4 is faster t…
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Database resources of the National Center for Biotechnology Information Open
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstra…
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Dali server update Open
The Dali server (http://ekhidna2.biocenter.helsinki.fi/dali) is a network service for comparing protein structures in 3D. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable…
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COG database update: focus on microbial diversity, model organisms, and widespread pathogens Open
The Clusters of Orthologous Genes (COG) database, also referred to as the Clusters of Orthologous Groups of proteins, was created in 1997 and went through several rounds of updates, most recently, in 2014. The current update, available at …
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Database Resources of the National Center for Biotechnology Information Open
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstrac…
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Uniclust databases of clustered and deeply annotated protein sequences and alignments Open
We present three clustered protein sequence databases, Uniclust90, Uniclust50, Uniclust30 and three databases of multiple sequence alignments (MSAs), Uniboost10, Uniboost20 and Uniboost30, as a resource for protein sequence analysis, funct…
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IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation Open
Intrinsically disordered proteins and protein regions (IDPs/IDRs) exist without a single well-defined conformation. They carry out important biological functions with multifaceted roles which is also reflected in their evolutionary behavio…
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Database resources of the National Center for Biotechnology Information Open
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstrac…
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InterPro: the protein sequence classification resource in 2025 Open
InterPro (https://www.ebi.ac.uk/interpro) is a freely accessible resource for the classification of protein sequences into families. It integrates predictive models, known as signatures, from multiple member databases to classify sequences…
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Ensembl comparative genomics resources Open
Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and ot…
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Database resources of the National Center for Biotechnology Information Open
The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstrac…
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FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes Open
FungiDB (fungidb.org) is a free online resource for data mining and functional genomics analysis for fungal and oomycete species. FungiDB is part of the Eukaryotic Pathogen Genomics Database Resource (EuPathDB, eupathdb.org) platform that …
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MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update) Open
MOLEonline is an interactive, web-based application for the detection and characterization of channels (pores and tunnels) within biomacromolecular structures. The updated version of MOLEonline overcomes limitations of the previous version…