The 50 most-cited articles in Nucleic Acids Research, 2024

The Interactive Tree Of Life (https://itol.embl.de) is an online tool for the management, display, annotation and manipulation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 6 introduces a modernized and completely rewritten user interface, together with numerous new features. A new dataset type has been introduced (colored/labeled ranges), greatly upgrading the functionality of the previous simple colored range annotation function. Additional annotation options have been implemented for several existing dataset types. Dataset template files now support simple assignment of annotations to multiple tree nodes through substring matching, including full regular expression support. Node metadata handling has been greatly extended with novel display and exporting options, and it can now be edited interactively or bulk updated through annotation files. Tree labels can be displayed using multiple simultaneous font styles, with precise positioning, sizing and styling of each individual label part. Various bulk label editing functions have been…

KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG…

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 describe ongoing changes to our production pipeline to limit the sequences available in UniProtKB to high-quality, non-redundant reference proteomes. We continue to manually curate the scientific literature to add the latest functional data and use machine learning techniques. We also encourage community curation to ensure key publications are not missed. We provide an update on the automatic annotation methods used by UniProtKB to predict information for unreviewed entries describing unstudied proteins. Finally, updates to the UniProt website are described, including a new tab linking protein to genomic information. In recognition of its value to the scientific community, the UniProt database has been awarded Global Core Biodata Resource status.

We introduce MetaboAnalyst version 6.0 as a unified platform for processing, analyzing, and interpreting data from targeted as well as untargeted metabolomics studies using liquid chromatography - mass spectrometry (LC-MS). The two main objectives in developing version 6.0 are to support tandem MS (MS2) data processing and annotation, as well as to support the analysis of data from exposomics studies and related experiments. Key features of MetaboAnalyst 6.0 include: (i) a significantly enhanced Spectra Processing module with support for MS2 data and the asari algorithm; (ii) a MS2 Peak Annotation module based on comprehensive MS2 reference databases with fragment-level annotation; (iii) a new Statistical Analysis module dedicated for handling complex study design with multiple factors or phenotypic descriptors; (iv) a Causal Analysis module for estimating metabolite - phenotype causal relations based on two-sample Mendelian randomization, and (v) a Dose-Response Analysis module for benchmark dose calculations. In addition, we have also improved MetaboAnalyst's visualization…

The PRoteomics IDEntifications (PRIDE) database (https://www.ebi.ac.uk/pride/) is the world's leading mass spectrometry (MS)-based proteomics data repository and one of the founding members of the ProteomeXchange consortium. This manuscript summarizes the developments in PRIDE resources and related tools for the last three years. The number of submitted datasets to PRIDE Archive (the archival component of PRIDE) has reached on average around 534 datasets per month. This has been possible thanks to continuous improvements in infrastructure such as a new file transfer protocol for very large datasets (Globus), a new data resubmission pipeline and an automatic dataset validation process. Additionally, we will highlight novel activities such as the availability of the PRIDE chatbot (based on the use of open-source Large Language Models), and our work to improve support for MS crosslinking datasets. Furthermore, we will describe how we have increased our efforts to reuse, reanalyze and disseminate high-quality proteomics data into added-value resources such as UniProt, Ensembl and…

High-quality schematic illustrations are fundamental to the publication of scientific achievements in biomedical research, which are crucial for effectively conveying complex biomedical concepts. However, creating such illustrations remains challenging for many researchers due to the need to devote a significant amount of time and effort to accomplish it. To address this need, we present the Generic Diagramming Platform (GDP, https://BioGDP.com), a comprehensive database of professionally crafted biomedical graphics (bio-graphics). Currently, GDP houses 7 562 high-quality bio-graphics, meticulously categorized into 10 major and 77 minor categories. To increase the design efficiency, GDP provides 204 customizable templates derived from an extensive review of over 2000 literature and 7 textbooks. With the interactive drawing platform and user-friendly web interface implemented in GDP, these resources can facilitate the efficient generation of publication-ready illustrations for the biomedical community. Additionally, GDP incorporates a collaborative submission system, allowing…

The EMBL-EBI Job Dispatcher sequence analysis tools framework (https://www.ebi.ac.uk/jdispatcher) enables the scientific community to perform a diverse range of sequence analyses using popular bioinformatics applications. Free access to the tools and required sequence datasets is provided through user-friendly web applications, as well as via RESTful and SOAP-based APIs. These are integrated into popular EMBL-EBI resources such as UniProt, InterPro, ENA and Ensembl Genomes. This paper overviews recent improvements to Job Dispatcher, including its brand new website and documentation, enhanced visualisations, improved job management, and a rising trend of user reliance on the service from low- and middle-income regions.

Interaction with chemicals, present in drugs, food, environments, and consumer goods, is an integral part of our everyday life. However, depending on the amount and duration, such interactions can also result in adverse effects. With the increase in computational methods, the in silico methods can offer significant benefits to both regulatory needs and requirements for risk assessments and the pharmaceutical industry to assess the safety profile of a chemical. Here, we present ProTox 3.0, which incorporates molecular similarity and machine-learning models for the prediction of 61 toxicity endpoints such as acute toxicity, organ toxicity, clinical toxicity, molecular-initiating events (MOE), adverse outcomes (Tox21) pathways, several other toxicological endpoints and toxicity off-targets. All the ProTox 3.0 models are validated on independent external sets and have shown strong performance. ProTox envisages itself as a complete, freely available computational platform for in silico toxicity prediction for toxicologists, regulatory agencies, computational chemists, and medicinal…

PubChem (https://pubchem.ncbi.nlm.nih.gov) is a large and highly-integrated public chemical database resource at NIH. In the past two years, significant updates were made to PubChem. With additions from over 130 new sources, PubChem contains >1000 data sources, 119 million compounds, 322 million substances and 295 million bioactivities. New interfaces, such as the consolidated literature panel and the patent knowledge panel, were developed. The consolidated literature panel combines all references about a compound into a single list, allowing users to easily find, sort, and export all relevant articles for a chemical in one place. The patent knowledge panels for a given query chemical or gene display chemicals, genes, and diseases co-mentioned with the query in patent documents, helping users to explore relationships between co-occurring entities within patent documents. PubChemRDF was expanded to include the co-occurrence data underlying the literature knowledge panel, enabling users to exploit semantic web technologies to explore entity relationships based on the co-occurrences in…

ADMETlab 3.0 is the second updated version of the web server that provides a comprehensive and efficient platform for evaluating ADMET-related parameters as well as physicochemical properties and medicinal chemistry characteristics involved in the drug discovery process. This new release addresses the limitations of the previous version and offers broader coverage, improved performance, API functionality, and decision support. For supporting data and endpoints, this version includes 119 features, an increase of 31 compared to the previous version. The updated number of entries is 1.5 times larger than the previous version with over 400 000 entries. ADMETlab 3.0 incorporates a multi-task DMPNN architecture coupled with molecular descriptors, a method that not only guaranteed calculation speed for each endpoint simultaneously, but also achieved a superior performance in terms of accuracy and robustness. In addition, an API has been introduced to meet the growing demand for programmatic access to large amounts of data in ADMETlab 3.0. Moreover, this version includes uncertainty…

Pharmacological modulation of RNA splicing by small molecules is an emerging facet of drug discovery. In this context, the SMN2 splicing modifier SMN-C5 was used as a prototype to understand the mode of action of small molecule splicing modifiers and propose the concept of 5'-splice site bulge repair. In this study, we combined in vitro binding assays and structure determination by NMR spectroscopy to identify the binding modes of four other small molecule splicing modifiers that switch the splicing of either the SMN2 or the HTT gene. Here, we determined the solution structures of risdiplam, branaplam, SMN-CX and SMN-CY bound to the intermolecular RNA helix epitope containing an unpaired adenine within the G-2A-1G+1U+2 motif of the 5'-splice site. Despite notable differences in their scaffolds, risdiplam, SMN-CX, SMN-CY and branaplam contact the RNA epitope similarly to SMN-C5, suggesting that the 5'-splice site bulge repair mechanism can be generalised. These findings not only deepen our understanding of the chemical diversity of splicing modifiers that target A-1 bulged 5'-splice…

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 into families and predict the presence of domains and significant sites. The InterPro database provides annotations for over 200 million sequences, ensuring extensive coverage of UniProtKB, the standard repository of protein sequences, and includes mappings to several other major resources, such as Gene Ontology (GO), Protein Data Bank in Europe (PDBe) and the AlphaFold Protein Structure Database. In this publication, we report on the status of InterPro (version 101.0), detailing new developments in the database, associated web interface and software. Notable updates include the increased integration of structures predicted by AlphaFold and the enhanced description of protein families using artificial intelligence. Over the past two years, more than 5000 new InterPro entries have been created. The InterPro website now offers access to 85 000…

Galaxy (https://galaxyproject.org) is deployed globally, predominantly through free-to-use services, supporting user-driven research that broadens in scope each year. Users are attracted to public Galaxy services by platform stability, tool and reference dataset diversity, training, support and integration, which enables complex, reproducible, shareable data analysis. Applying the principles of user experience design (UXD), has driven improvements in accessibility, tool discoverability through Galaxy Labs/subdomains, and a redesigned Galaxy ToolShed. Galaxy tool capabilities are progressing in two strategic directions: integrating general purpose graphical processing units (GPGPU) access for cutting-edge methods, and licensed tool support. Engagement with global research consortia is being increased by developing more workflows in Galaxy and by resourcing the public Galaxy services to run them. The Galaxy Training Network (GTN) portfolio has grown in both size, and accessibility, through learning paths and direct integration with Galaxy tools that feature in training courses. Code…

Ensembl (www.ensembl.org) is an open platform integrating publicly available genomics data across the tree of life with a focus on eukaryotic species related to human health, agriculture and biodiversity. This year has seen a continued expansion in the number of species represented, with >4800 eukaryotic and >31 300 prokaryotic genomes available. The new Ensembl site, currently in beta, has continued to develop, currently holding >2700 eukaryotic genome assemblies. The new site provides genome, gene, transcript, homology and variation views, and will replace the current Rapid Release site; this represents a key step towards provision of a single integrated Ensembl site. Additional activities have included developing improved regulatory annotation for human, mouse and agricultural species, and expanding the Ensembl Variant Effect Predictor tool. To learn more about Ensembl, help and documentation are available along with an extensive training program that can be accessed via our training pages.

Proteins cooperate, regulate and bind each other to achieve their functions. Understanding the complex network of their interactions is essential for a systems-level description of cellular processes. The STRING database compiles, scores and integrates protein-protein association information drawn from experimental assays, computational predictions and prior knowledge. Its goal is to create comprehensive and objective global networks that encompass both physical and functional interactions. Additionally, STRING provides supplementary tools such as network clustering and pathway enrichment analysis. The latest version, STRING 12.5, introduces a new 'regulatory network', for which it gathers evidence on the type and directionality of interactions using curated pathway databases and a fine-tuned language model parsing the literature. This update enables users to visualize and access three distinct network types-functional, physical and regulatory-separately, each applicable to distinct research needs. In addition, the pathway enrichment detection functionality has been updated, with…

The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource for genomics and bioinformatics research. Annotation data available on Genome Browser includes both internally created and maintained tracks as well as custom tracks and track hubs provided by the research community. This last year's updates include over 25 new annotation tracks such as the gnomAD 4.1 track on the human GRCh38/hg38 assembly, the addition of three new public hubs, and significant expansions to the Genome Archive[GenArk) system for interacting with the enormous variety of assemblies. We have also made improvements to our interface, including updates to the browser graphic page, such as a new popup dialog feature that now displays item details without requiring navigation away from the main Genome Browser page. GenePred tracks have been upgraded with right-click options for zooming and precise navigation, along with…

The National Center for Biotechnology Information (NCBI) provides online information resources for biology, including the GenBank® nucleic acid sequence repository and the PubMed® repository of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 31 distinct repositories and knowledgebases. The E-utilities serve as the programming interface for most of these. Resources receiving significant updates in the past year include PubMed, PubMed Central, Bookshelf, the NIH Comparative Genomics Resource, BLAST, Sequence Read Archive, Taxonomy, iCn3D, Conserved Domain Database, Pathogen Detection, antimicrobial resistance resources and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

Drug discovery aims to identify potential therapeutic compounds capable of modulating the activity of specific biological targets. Molecular docking can efficiently support this process by predicting binding interactions between small molecules and macromolecular targets and potentially accelerating screening campaigns. SwissDock is a computational tool released in 2011 as part of the SwissDrugDesign project, providing a free web-based service for small-molecule docking after automatized preparation of ligands and targets. Here, we present the latest version of SwissDock, in which EADock DSS has been replaced by two state-of-the-art docking programs, i.e. Attracting Cavities and AutoDock Vina. AutoDock Vina provides faster docking predictions, while Attracting Cavities offers more accurate results. Ligands can be imported in various ways, including as files, SMILES notation or molecular sketches. Targets can be imported as PDB files or identified by their PDB ID. In addition, advanced search options are available both for ligands and targets, giving users automatized access to…

The NHGRI-EBI GWAS Catalog serves as a vital resource for the genetic research community, providing access to the most comprehensive database of human GWAS results. Currently, it contains close to 7 000 publications for >15 000 traits, from which more than 625 000 lead associations have been curated. Additionally, 85 000 full genome-wide summary statistics datasets-containing association data for all variants in the analysis-are available for downstream analyses such as meta-analysis, fine-mapping, Mendelian randomisation or development of polygenic risk scores. As a centralised repository for GWAS results, the GWAS Catalog sets and implements standards for data submission and harmonisation, and encourages the use of consistent descriptors for traits, samples and methodologies. We share processes and vocabulary with the PGS Catalog, improving interoperability for a growing user group. Here, we describe the latest changes in data content, improvements in our user interface, and the implementation of the GWAS-SSF standard format for summary statistics. We address the challenges of…

GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species' genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate…

The National Genomics Data Center (NGDC), which is a part of the China National Center for Bioinformation (CNCB), offers a comprehensive suite of database resources to support the global scientific community. Amidst the unprecedented accumulation of multi-omics data, CNCB-NGDC is committed to continually evolving and updating its core database resources through big data archiving, integrative analysis and value-added curation. Over the past year, CNCB-NGDC has expanded its collaborations with international databases and established new subcenters focusing on biodiversity, traditional Chinese medicine and tumor genetics. Substantial efforts have been made toward encompassing a broad spectrum of multi-omics data, developing innovative resources and enhancing existing resources. Notably, new resources have been developed for single-cell omics (scTWAS Atlas), genome and variation (VDGE), health and disease (CVD Atlas, CPMKG, Immunosenescence Inventory, HemAtlas, Cyclicpepedia, IDeAS), biodiversity and biosynthesis (RefMetaPlant, MASH-Ocean) and research tools (CCLHunter). All resources…

Enrichment analysis, crucial for interpreting genomic, transcriptomic, and proteomic data, is expanding into metabolomics. Furthermore, there is a rising demand for integrated enrichment analysis that combines data from different studies and omics platforms, as seen in meta-analysis and multi-omics research. To address these growing needs, we have updated WebGestalt to include enrichment analysis capabilities for both metabolites and multiple input lists of analytes. We have also significantly increased analysis speed, revamped the user interface, and introduced new pathway visualizations to accommodate these updates. Notably, the adoption of a Rust backend reduced gene set enrichment analysis time by 95% from 270.64 to 12.41 s and network topology-based analysis by 89% from 159.59 to 17.31 s in our evaluation. This performance improvement is also accessible in both the R package and a newly introduced Python package. Additionally, we have updated the data in the WebGestalt database to reflect the current status of each source and have expanded our collection of pathways, networks,…

Hundreds of millions of single cells have been analyzed using high-throughput transcriptomic methods. The cumulative knowledge within these datasets provides an exciting opportunity for unlocking insights into health and disease at the level of single cells. Meta-analyses that span diverse datasets building on recent advances in large language models and other machine-learning approaches pose exciting new directions to model and extract insight from single-cell data. Despite the promise of these and emerging analytical tools for analyzing large amounts of data, the sheer number of datasets, data models and accessibility remains a challenge. Here, we present CZ CELLxGENE Discover (cellxgene.cziscience.com), a data platform that provides curated and interoperable single-cell data. Available via a free-to-use online data portal, CZ CELLxGENE hosts a growing corpus of community-contributed data of over 93 million unique cells. Curated, standardized and associated with consistent cell-level metadata, this collection of single-cell transcriptomic data is the largest of its kind and…

OrthoDB (https://www.orthodb.org) offers evolutionary and functional annotations of orthologous genes in the widest sampling of eukaryotes, prokaryotes, and viruses, extending experimental gene function knowledge to newly sequenced genomes. We collect gene annotations, delineate hierarchical gene orthology and annotate the orthologous groups (OGs) with functional and evolutionary traits. OrthoDB is the leading resource for species diversity, striving to sample the most diverse and well-researched organisms with the highest quality genomic data. This update expands to include 5827 eukaryotic genomes. We have also added coding DNA sequences (CDSs) and gene loci coordinates. OrthoDB can be browsed, downloaded, or accessed using REST API, SPARQL/RDF and now also via API packages for Python and R Bioconductor. OrthoLoger (https://orthologer.ezlab.org), the tool used for inferring orthologs in OrthoDB, is now available as a Conda package and through BioContainers. ODB-mapper, a component of OrthoLoger, streamlines annotation of genes from newly sequenced genomes with OrthoDB evolutionary…

The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.uk/interpro/). This update describes major developments in Pfam since 2020, including decommissioning the Pfam website and integration with InterPro, harmonization with the ECOD structural classification, and expanded curation of metagenomic, microprotein and repeat-containing families. We highlight how AlphaFold structure predictions are being leveraged to refine domain boundaries and identify new domains. New families discovered through large-scale sequence similarity analysis of AlphaFold models are described. We also detail the development of Pfam-N, which uses deep learning to expand family coverage, achieving an 8.8% increase in UniProtKB coverage compared to standard Pfam. We discuss plans for more frequent Pfam releases integrated with InterPro and the potential for artificial intelligence to further assist curation. Despite recent advances, many protein families remain to be classified,…

Evaluating pharmacokinetic properties of small molecules is considered a key feature in most drug development and high-throughput screening processes. Generally, pharmacokinetics, which represent the fate of drugs in the human body, are described from four perspectives: absorption, distribution, metabolism and excretion-all of which are closely related to a fifth perspective, toxicity (ADMET). Since obtaining ADMET data from in vitro, in vivo or pre-clinical stages is time consuming and expensive, many efforts have been made to predict ADMET properties via computational approaches. However, the majority of available methods are limited in their ability to provide pharmacokinetics and toxicity for diverse targets, ensure good overall accuracy, and offer ease of use, interpretability and extensibility for further optimizations. Here, we introduce Deep-PK, a deep learning-based pharmacokinetic and toxicity prediction, analysis and optimization platform. We applied graph neural networks and graph-based signatures as a graph-level feature to yield the best predictive performance across…

Reference sequences and annotations serve as the foundation for many lines of research today, from organism and sequence identification to providing a core description of the genes, transcripts and proteins found in an organism's genome. Interpretation of data including transcriptomics, proteomics, sequence variation and comparative analyses based on reference gene annotations informs our understanding of gene function and possible disease mechanisms, leading to new biomedical discoveries. The Reference Sequence (RefSeq) resource created at the National Center for Biotechnology Information (NCBI) leverages both automatic processes and expert curation to create a robust set of reference sequences of genomic, transcript and protein data spanning the tree of life. RefSeq continues to refine its annotation and quality control processes and utilize better quality genomes resulting from advances in sequencing technologies as well as RNA-Seq data to produce high-quality annotated genomes, ortholog predictions across more organisms and other products that are easily accessible through…

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, RCSB.org), the US Worldwide Protein Data Bank (wwPDB, wwPDB.org) data center for the global PDB archive, provides access to the PDB data via its RCSB.org research-focused web portal. We report substantial additions to the tools and visualization features available at RCSB.org, which now delivers more than 227000 experimentally determined atomic-level three-dimensional (3D) biostructures stored in the global PDB archive alongside more than 1 million Computed Structure Models (CSMs) of proteins (including models for human, model organisms, select human pathogens, crop plants and organisms important for addressing climate change). In addition to providing support for 3D structure motif searches with user-provided coordinates, new features highlighted herein include query results organized by redundancy-reduced Groups and summary pages that facilitate exploration of groups of similar proteins. Newly released programmatic tools are also described, as are enhanced training opportunities.

Over the past 20 years, the Immune Epitope Database (IEDB, iedb.org) has established itself as the foremost resource for immune epitope data. The IEDB catalogs published epitopes and their contextual experimental data in a freely searchable public resource. The IEDB team manually curates data from the literature into a structured format and spans infectious, allergic, autoimmune, and transplant diseases. Here, we describe the enhancements made since our 2018 paper, capturing user-directed updates to the search interface, advanced data exports, increases in data quality, and improved interoperability across related resources. As we look forward to the next 20 years, we are confident in our ability to meet the needs of our users and to contribute to the broader field of data standardization.

With the escalating crisis of bacterial multidrug resistance, anti-virulence therapeutic strategies have emerged as a highly promising alternative to conventional antibiotic treatments. Anti-virulence compounds are specifically designed to target virulence factors (VFs), disarming pathogens without affecting bacterial growth and thus reduce the selective pressure for resistance development. However, due to the complexity of bacterial pathogenesis, no anti-virulence small molecules have been approved for clinical use thus far, despite the documentation of hundreds of potential candidates. To provide valuable reference resources for drug design, repurposing, and target selection, the virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) has systematically collected public data on anti-virulence compounds through extensive literature mining, and further integrated this information with its existing knowledge of bacterial VFs. To date, the VFDB has curated a comprehensive dataset of 902 anti-virulence compounds across 17 superclasses reported by 262 studies worldwide. By…

MicroRNAs (miRNAs) are small non-coding RNAs (18-26 nucleotides) that regulate gene expression by interacting with target mRNAs, affecting various physiological and pathological processes. miRTarBase, a database of experimentally validated miRNA-target interactions (MTIs), now features over 3 817 550 validated MTIs from 13 690 articles, significantly expanding its previous version. The updated database includes miRNA interactions with therapeutic agents, revealing roles in drug resistance and therapeutic strategies. It also highlights miRNAs as predictive, safety and monitoring biomarkers for toxicity assessment, clinical treatment guidance and therapeutic optimization. The expansion of miRNA-mRNA and miRNA-miRNA networks allows the identification of key regulatory genes and co-regulatory miRNAs, providing deeper insights into miRNA functions and critical target genes. Information on oxidized miRNA sequences has been added, shedding light on how oxidative modifications influence miRNA targeting and regulation. The integration of the LLAMA3 model into the NLP pipeline, alongside…

Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using…

For 20 years, the Comparative Toxicogenomics Database (CTD; https://ctdbase.org) has provided high-quality, literature-based curated content describing how environmental chemicals affect human health. Today, CTD includes over 94 million toxicogenomic connections relating chemicals, genes/proteins, phenotypes, anatomical terms, diseases, comparative species, pathways and exposures. In this 20th year anniversary update, we reflect on CTD's remarkable growth and provide an overview of the increased data content and new features, including enhancements to the curation workflow (e.g. new exposure curation tool and expanded use of natural language processing), added functionality (e.g. improvements to CTD Tetramers and Pathway View tools) and significant upgrades to software and infrastructure. Linking lab-based core curation with real-world human exposure curation via the use of controlled vocabularies facilitates analysis of content across the entire environmental health continuum, from molecular toxicological mechanisms to the population level, and vice versa. The 'prototype database'…

BindingDB (bindingdb.org) is a public, web-accessible database of experimentally measured binding affinities between small molecules and proteins, which supports diverse applications including medicinal chemistry, biochemical pathway annotation, training of artificial intelligence models and computational chemistry methods development. This update reports significant growth and enhancements since our last review in 2016. Of note, the database now contains 2.9 million binding measurements spanning 1.3 million compounds and thousands of protein targets. This growth is largely attributable to our unique focus on curating data from US patents, which has yielded a substantial influx of novel binding data. Recent improvements include a remake of the website following responsive web design principles, enhanced search and filtering capabilities, new data download options and webservices and establishment of a long-term data archive replicated across dispersed sites. We also discuss BindingDB's positioning relative to related resources, its open data sharing policies, insights gleaned from…

DeepLoc 2.0 is a popular web server for the prediction of protein subcellular localization and sorting signals. Here, we introduce DeepLoc 2.1, which additionally classifies the input proteins into the membrane protein types Transmembrane, Peripheral, Lipid-anchored and Soluble. Leveraging pre-trained transformer-based protein language models, the server utilizes a three-stage architecture for sequence-based, multi-label predictions. Comparative evaluations with other established tools on a test set of 4933 eukaryotic protein sequences, constructed following stringent homology partitioning, demonstrate state-of-the-art performance. Notably, DeepLoc 2.1 outperforms existing models, with the larger ProtT5 model exhibiting a marginal advantage over the ESM-1B model. The web server is available at https://services.healthtech.dtu.dk/services/DeepLoc-2.1.

The Open Targets Platform (https://platform.opentargets.org) is a unique, open-source, publicly-available knowledge base providing data and tooling for systematic drug target identification, annotation, and prioritisation. Since our last report, we have expanded the scope of the Platform through a number of significant enhancements and data updates, with the aim to enable our users to formulate more flexible and impactful therapeutic hypotheses. In this context, we have completely revamped our target-disease associations page with more interactive facets and built-in functionalities to empower users with additional control over their experience using the Platform, and added a new Target Prioritisation view. This enables users to prioritise targets based upon clinical precedence, tractability, doability and safety attributes. We have also implemented a direction of effect assessment for eight sources of target-disease association evidence, showing the effect of genetic variation on the function of a target is associated with risk or protection for a trait to inform on potential…

ChIP-Atlas (https://chip-atlas.org/) presents a suite of data-mining tools for analyzing epigenomic landscapes, powered by the comprehensive integration of over 376 000 public ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments from six representative model organisms. To unravel the intricacies of chromatin architecture that mediates the regulome-initiated generation of transcriptional and phenotypic diversity within cells, we report ChIP-Atlas 3.0 that enhances clarity by incorporating additional tracks for genomic and epigenomic features within a newly consolidated 'annotation track' section. The tracks include chromosomal conformation (Hi-C and eQTL datasets), transcriptional regulatory elements (ChromHMM and FANTOM5 enhancers), and genomic variants associated with diseases and phenotypes (GWAS SNPs and ClinVar variants). These annotation tracks are easily accessible alongside other experimental tracks, facilitating better elucidation of chromatin architecture underlying the diversification of transcriptional and phenotypic traits. Furthermore, 'Diff Analysis,' a new…

The process of induced pluripotent stem cells (iPSCs) reprogramming involves several crucial events, including the mesenchymal-epithelial transition (MET), activation of pluripotent genes, metabolic reprogramming, and epigenetic rewiring. Although these events intricately interact and influence each other, the specific element that regulates the reprogramming network remains unclear. Dux, a factor known to promote totipotency during the transition from embryonic stem cells (ESC) to 2C-like ESC (2CLC), has not been extensively studied in the context of iPSC reprogramming. In this study, we demonstrate that the modification of H3K18la induced by Dux overexpression controls the metabolism-H3K18la-MET network, enhancing the efficiency of iPSC reprogramming through a metabolic switch and the recruitment of p300 via its C-terminal domain. Furthermore, our proteomic analysis of H3K18la immunoprecipitation experiment uncovers the specific recruitment of Brg1 during reprogramming, with both H3K18la and Brg1 being enriched on the promoters of genes associated with pluripotency and epithelial…

Absorption, distribution, metabolism, excretion and toxicity (ADMET) properties play a crucial role in drug discovery and chemical safety assessment. Built on the achievements of admetSAR and its successor, admetSAR2.0, this paper introduced the new version of the series, admetSAR3.0, as a comprehensive platform for chemical ADMET assessment, including search, prediction and optimization modules. In the search module, admetSAR3.0 hosted over 370 000 high-quality experimental ADMET data for 104 652 unique compounds, and supplemented chemical structure similarity search function to facilitate read-across. In the prediction module, we introduced comprehensive ADMET endpoints and two new sections for environmental and cosmetic risk assessments, empowering admetSAR3.0 to provide prediction for 119 endpoints, more than double numbers compared to the previous version. Furthermore, the advanced multi-task graph neural network framework offered robust and reliable support for ADMET prediction. In particular, a module named ADMETopt was added to automatically optimize the ADMET properties of…

The Rfam database, a widely used repository of non-coding RNA families, has undergone significant updates in release 15.0. This paper introduces major improvements, including the expansion of Rfamseq to 26 106 genomes, a 76% increase, incorporating the latest UniProt reference proteomes and additional viral genomes. Sixty-five RNA families were enhanced using experimentally determined 3D structures, improving the accuracy of consensus secondary structures and annotations. R-scape covariation analysis was used to refine structural predictions in 26 families. Gene Ontology (GO) and Sequence Ontology annotations were comprehensively updated, increasing GO term coverage to 75% of families. The release adds 14 new Hepatitis C Virus RNA families and completes microRNA family synchronization with miRBase, resulting in 1603 microRNA families. New data types, including FULL alignments, have been implemented. Integration with APICURON for improved curator attribution and multiple website enhancements further improve user experience. These updates significantly expand Rfam's coverage and…

Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important biological functions without relying on a single well-defined conformation. As these proteins are a challenge to study experimentally, computational methods play important roles in their characterization. One of the commonly used tools is the IUPred web server which provides prediction of disordered regions and their binding sites. IUPred is rooted in a simple biophysical model and uses a limited number of parameters largely derived on globular protein structures only. This enabled an incredibly fast and robust prediction method, however, its limitations have also become apparent in light of recent breakthrough methods using deep learning techniques. Here, we present AIUPred, a novel version of IUPred which incorporates deep learning techniques into the energy estimation framework. It achieves improved performance while keeping the robustness of the original method. Based on the evaluation of recent benchmark datasets, AIUPred scored amongst the top three single sequence based methods. With a new…

Geometric and topological properties of protein structures, including surface pockets, interior cavities and cross channels, are of fundamental importance for proteins to carry out their functions. Computed Atlas of Surface Topography of proteins (CASTp) is a widely used web server for locating, delineating, and measuring these geometric and topological properties of protein structures. Recent developments in AI-based protein structure prediction such as AlphaFold2 (AF2) have significantly expanded our knowledge on protein structures. Here we present CASTpFold, a continuation of CASTp that provides accurate and comprehensive identifications and quantifications of protein topography. It now provides (i) results on an expanded database of proteins, including the Protein Data Bank (PDB) and non-singleton representative structures of AlphaFold2 structures, covering 183 million AF2 structures; (ii) functional pockets prediction with corresponding Gene Ontology (GO) terms or Enzyme Commission (EC) numbers for AF2-predicted structures and (iii) pocket similarity search function for surface…

PubTator 3.0 (https://www.ncbi.nlm.nih.gov/research/pubtator3/) is a biomedical literature resource using state-of-the-art AI techniques to offer semantic and relation searches for key concepts like proteins, genetic variants, diseases and chemicals. It currently provides over one billion entity and relation annotations across approximately 36 million PubMed abstracts and 6 million full-text articles from the PMC open access subset, updated weekly. PubTator 3.0's online interface and API utilize these precomputed entity relations and synonyms to provide advanced search capabilities and enable large-scale analyses, streamlining many complex information needs. We showcase the retrieval quality of PubTator 3.0 using a series of entity pair queries, demonstrating that PubTator 3.0 retrieves a greater number of articles than either PubMed or Google Scholar, with higher precision in the top 20 results. We further show that integrating ChatGPT (GPT-4) with PubTator APIs dramatically improves the factuality and verifiability of its responses. In summary, PubTator 3.0 offers a comprehensive…

The COCONUT (COlleCtion of Open Natural prodUcTs) database was launched in 2021 as an aggregation of openly available natural product datasets and has been one of the biggest open natural product databases since. Apart from the chemical structures of natural products, COCONUT contains information about names and synonyms, species and organism parts in which the natural product has been found, geographic information about where the respective sample has been collected and literature references, where available. COCONUT is openly accessible at https://coconut.naturalproducts.net. Users can search textual information and perform structure, substructure, and similarity searches. The data in COCONUT are available for bulk download as SDF, CSV and a database dump. The web application for accessing the data is open-source. Here, we describe COCONUT 2.0, for which the web application has been completely rewritten, and the data have been newly assembled and extensively curated. New features include data submissions by users and community curation facilitated in various ways.

ClinVar (www.ncbi.nlm.nih.gov/clinvar/) is a free, public database of human genetic variants and their relationships to disease, with >3 million variants submitted by >2800 organizations across the world. The database was recently updated to have three types of classifications: germline, oncogenicity and clinical impact for somatic variants. As for germline variants, classifications for somatic variants can be submitted in batches in a file submission or through the submission API; variants can also be submitted and updated one at a time in online submission forms. The ClinVar XML files were redesigned to allow multiple classification types. Both old and new formats of the XML are supported through the end of 2024. Data for somatic classifications were also added to the ClinVar VCF files and to several tab-delimited files. The ClinVar VCV pages were updated to display the three types of classifications, both as it was submitted and as it was aggregated by ClinVar. Clinical testing laboratories and others in the cancer community are invited to share their classifications of somatic…

The Single Nucleotide Polymorphism Database (dbSNP), established in 1998 by the National Center for Biotechnology Information (NCBI), has been a critical resource in genomics for cataloging small genetic variations. Originally focused on single nucleotide polymorphisms (SNPs), dbSNP has since expanded to include a variety of genetic variants, playing a key role in genome-wide association studies (GWAS), population genetics, pharmacogenomics, and cancer research. Over 25 years, dbSNP has grown to include more than 4.4 billion submitted SNPs and 1.1 billion unique reference SNPs, providing essential data for identifying disease-related genetic variants and studying human diversity. Integrating large-scale projects like 1000 Genomes, gnomAD, TOPMed, and ALFA has expanded dbSNP's catalog of human genetic variation, increasing its usefulness for research and clinical applications. Keeping up with advancements such as next-generation sequencing and cloud-based infrastructure, dbSNP remains a cornerstone of genetic research supporting continued discoveries in precision medicine and…

The Clusters of Orthologous Genes (COG) database, originally created in 1997, has been updated to reflect the constantly growing collection of completely sequenced prokaryotic genomes. This update increased the genome coverage from 1309 to 2296 species, including 2103 bacteria and 193 archaea, in most cases, with a single representative genome per genus. This set covers all genera of bacteria and archaea that included organisms with 'complete genomes' as per NCBI databases in November 2023. The number of COGs has been expanded from 4877 to 4981, primarily by including protein families involved in bacterial protein secretion. Accordingly, COG pathways and functional groups now include secretion systems of types II through X, as well as Flp/Tad and type IV pili. These groupings allow straightforward identification and examination of the prokaryotic lineages that encompass-or lack-a particular secretion system. Other developments include improved annotations for the rRNA and tRNA modification proteins, multi-domain signal transduction proteins, and some previously uncharacterized…

In 2025, the bacterial diversity database BacDive is the leading database for strain-level bacterial and archaeal information. It has been selected as an ELIXIR Core Data Resource as well as a Global Core Biodata Resource. Since its initial release more than ten years ago, BacDive (https://bacdive.dsmz.de) has grown tremendously in content and functionalities, and is a comprehensive resource covering the phenotypic diversity of prokaryotes with data on taxonomy, morphology, physiology, cultivation, and more. The current release (2023.2) contains 2.6 million data points on 97 334 strains, reflecting an increase by 52% since the previous publication in 2021. This remarkable growth can largely be attributed to the integration of the world-wide largest collection of Analytical Profile Index (API) test results, which are now fully integrated into the database and searchable. A novel BacDive knowledge graph provides powerful search options through a SPARQL endpoint, including the possibility for federated searches across multiple data sources. The high-quality data provided by BacDive is…

By processing and abstracting diverse omics datasets into associations between genes and their attributes, the Harmonizome database enables researchers to explore and integrate knowledge about human genes from many central omics resources. Here, we introduce Harmonizome 3.0, a significant upgrade to the original Harmonizome database. The upgrade adds 26 datasets that contribute nearly 12 million associations between genes and various attribute types such as cells and tissues, diseases, and pathways. The upgrade has a dataset crossing feature to identify gene modules that are shared across datasets. To further explain significantly high gene set overlap between dataset pairs, a large language model (LLM) composes a paragraph that speculates about the reasons behind the high overlap. The upgrade also adds more data formats and visualization options. Datasets are downloadable as knowledge graph (KG) assertions and visualized with Uniform Manifold Approximation and Projection (UMAP) plots. The KG assertions can be explored via a user interface that visualizes gene-attribute associations…

GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public data repository that contains 34 trillion base pairs from over 4.7 billion nucleotide sequences for 581 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage. We summarize the content of the database in 2025 and recent updates such as accelerated processing of influenza sequences and the ability to upload feature tables to Submission Portal for messenger RNA sequences. We provide an overview of the web, application programming and command-line interfaces that allow users to access GenBank data. We also discuss the importance of creating BioProject and BioSample records during submissions, particularly for viruses and metagenomes. Finally, we summarize educational materials and recent community outreach efforts.