Nucleic Acids Research

Article	Citations
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation	6420
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets	4962
UniProt: the universal protein knowledgebase in 2021	4928
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models	4861
The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences	3818
MetaboAnalyst 5.0: narrowing the gap between raw spectra and functional insights	2732
The Gene Ontology resource: enriching a GOld mine	2604
DAVID: a web server for functional enrichment analysis and functional annotation of gene lists (2021 update)	2553
UniProt: the Universal Protein Knowledgebase in 2023	2451
PubChem in 2021: new data content and improved web interfaces	2367
KEGG for taxonomy-based analysis of pathways and genomes	2169
The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest	1981
antiSMASH 6.0: improving cluster detection and comparison capabilities	1757
The InterPro protein families and domains database: 20 years on	1565
Search and sequence analysis tools services from EMBL-EBI in 2022	1518
Ensembl 2022	1391
Database resources of the national center for biotechnology information	1347
Ensembl 2021	1316
ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties	1252
The reactome pathway knowledgebase 2022	1243
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles	1174
The carbohydrate-active enzyme database: functions and literature	1135
InterPro in 2022	1116
PubChem 2023 update	1072
HMDB 5.0: the Human Metabolome Database for 2022	1046

PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API	1045
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bio	1036
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes	991
KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis	964
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations	954
GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy	954
PLIP 2021: expanding the scope of the protein–ligand interaction profiler to DNA and RNA	916
GENCODE 2021	820
The Human Phenotype Ontology in 2021	773
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes	759
RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation	645
Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures	634
The IPD-IMGT/HLA Database	627
Rfam 14: expanded coverage of metagenomic, viral and microRNA families	614
antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation	613
VFDB 2022: a general classification scheme for bacterial virulence factors	607
The NHGRI-EBI GWAS Catalog: knowledgebase and deposition resource	604
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment	601
WikiPathways: connecting communities	593
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update	554
COG database update: focus on microbial diversity, model organisms, and widespread pathogens	546
Dali server: structural unification of protein families	543
Integration of the Drug–Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts	542
CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database	489
MODOMICS: a database of RNA modification pathways. 2021 update	484
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022	465
miRTarBase update 2022: an informative resource for experimentally validated miRNA–target interactions	456
Ensembl 2023	454
Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users	428
BRENDA, the ELIXIR core data resource in 2021: new developments and updates	426
SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes	413
Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR	405
Therapeutic target database update 2022: facilitating drug discovery with enriched comparative data of targeted agents	390
Proksee: in-depth characterization and visualization of bacterial genomes	386
CB-Dock2: improved protein–ligand blind docking by integrating cavity detection, docking and homologous template fitting	384
FlyBase: updates to theDrosophila melanogasterknowledge base	383
The UCSC Genome Browser database: 2021 update	377
IUPred3: prediction of protein disorder enhanced with unambiguous experimental annotation and visualization of evolutionary conservation	331
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center	328
iProX in 2021: connecting proteomics data sharing with big data	323
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine	320
CATH: increased structural coverage of functional space	319
Open Targets Platform: supporting systematic drug–target identification and prioritisation	310
The ProteomeXchange consortium at 10 years: 2023 update	303
DBAASP v3: database of antimicrobial/cytotoxic activity and structure of peptides as a resource for development of new therapeutics	303
g:Profiler—interoperable web service for functional enrichment analysis and gene identifier mapping (2023 update)	292
RCSB Protein Data Bank (RCSB.org): delivery of experimentally-determined PDB structures alongside one million computed structure models of proteins from artificial intelligence/machine learning	290
CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data	287
Genenames.org: the HGNC and VGNC resources in 2021	283
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models	283

GPCRdb in 2021: integrating GPCR sequence, structure and function	280
GEPIA2021: integrating multiple deconvolution-based analysis into GEPIA	270
IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses	267
Comparative Toxicogenomics Database (CTD): update 2023	266
Correction to ‘The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets’	266
Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology	264
The UCSC Genome Browser database: 2023 update	257
webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study	255
A comprehensive review of m6A/m6Am RNA methyltransferase structures	249
The Transporter Classification Database (TCDB): 2021 update	244
Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees	242
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples	239
ReMap 2022: a database of Human, Mouse, Drosophila and Arabidopsis regulatory regions from an integrative analysis of DNA-binding sequencing experiments	233
The conserved domain database in 2023	230
Chemistry, structure and function of approved oligonucleotide therapeutics	225
Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements	216
GenBank	210
The UCSC Genome Browser database: 2022 update	207
Ensembl Genomes 2022: an expanding genome resource for non-vertebrates	196
MobiDB: intrinsically disordered proteins in 2021	195
LitCovid: an open database of COVID-19 literature	194
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants	193
dbCAN3: automated carbohydrate-active enzyme and substrate annotation	193
Database resources of the National Center for Biotechnology Information in 2023	192
ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data	191
The Eukaryotic Linear Motif resource: 2022 release	187
Lnc2Cancer 3.0: an updated resource for experimentally supported lncRNA/circRNA cancer associations and web tools based on RNA-seq and scRNA-seq data	187
MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters	186
The Sequence Read Archive: a decade more of explosive growth	176
The International Mouse Phenotyping Consortium: comprehensive knockout phenotyping underpinning the study of human disease	174
DNA G-quadruplex structures: more than simple roadblocks to transcription?	172
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021	168
Genenames.org: the HGNC resources in 2023	166
GTRD: an integrated view of transcription regulation	166
MutationTaster2021	165
PredictProtein - Predicting Protein Structure and Function for 29 Years	164
BeStSel: webserver for secondary structure and fold prediction for protein CD spectroscopy	163
Bringing the Animal QTLdb and CorrDB into the future: meeting new challenges and providing updated services	163
The next-generation Open Targets Platform: reimagined, redesigned, rebuilt	161
OrthoDB v11: annotation of orthologs in the widest sampling of organismal diversity	161
OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more	158
Genomes OnLine Database (GOLD) v.8: overview and updates	156
Interactive Tree of Life (iTOL) v6: recent updates to the phylogenetic tree display and annotation tool	154
The international nucleotide sequence database collaboration	152
iLearnPlus:a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization	151
The Natural Products Atlas 2.0: a database of microbially-derived natural products	147
TISCH2: expanded datasets and new tools for single-cell transcriptome analyses of the tumor microenvironment	147
AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences	147
FerrDb V2: update of the manually curated database of ferroptosis regulators and ferroptosis-disease associations	143
GenBank	142
DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial peptides	142
CellCall: integrating paired ligand–receptor and transcription factor activities for cell–cell communication	141
Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy	139
The IntAct database: efficient access to fine-grained molecular interaction data	138
IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata	138
DrugCentral 2021 supports drug discovery and repositioning	137
ProThermDB: thermodynamic database for proteins and mutants revisited after 15 years	135
The Human Disease Ontology 2022 update	135
The IMG/M data management and analysis system v.7: content updates and new features	135
OncoDB: an interactive online database for analysis of gene expression and viral infection in cancer	133
GenBank 2024 Update	131
The Reactome Pathway Knowledgebase 2024	130
PLAZA 5.0: extending the scope and power of comparative and functional genomics in plants	129
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023	129
DisProt in 2022: improved quality and accessibility of protein intrinsic disorder annotation	126
CellMiner Cross-Database (CellMinerCDB) version 1.2: Exploration of patient-derived cancer cell line pharmacogenomics	125
OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes	125
OrthoDB in 2020: evolutionary and functional annotations of orthologs	125
MGnify: the microbiome sequence data analysis resource in 2023	125
TCRD and Pharos 2021: mining the human proteome for disease biology	122
PLSDB: advancing a comprehensive database of bacterial plasmids	120
MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data	120
GENCODE: reference annotation for the human and mouse genomes in 2023	119
jMorp updates in 2020: large enhancement of multi-omics data resources on the general Japanese population	119
BRAD V3.0: an upgraded Brassicaceae database	118
NetSurfP-3.0: accurate and fast prediction of protein structural features by protein language models and deep learning	117
Post-translational modification of RNA m6A demethylase ALKBH5 regulates ROS-induced DNA damage response	117
The current state of SubtiWiki, the database for the model organism Bacillus subtilis	116
The IUPHAR/BPS guide to PHARMACOLOGY in 2022: curating pharmacology for COVID-19, malaria and antibacterials	116
The ChEMBL Database in 2023: a drug discovery platform spanning multiple bioactivity data types and time periods	116

Properties and biological impact of RNA G-quadruplexes: from order to turmoil and back	116
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility	115
Expression Atlas update: gene and protein expression in multiple species	115
DrugBank 6.0: the DrugBank Knowledgebase for 2024	113
The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes	113
RNA G-quadruplexes (rG4s): genomics and biological functions	112
Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types	112
BioSeq-BLM: a platform for analyzing DNA, RNA and protein sequences based on biological language models	111
JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles	111
Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release	111
A unified model for the G1/S cell cycle transition	110
The European Nucleotide Archive in 2020	110
BacDive in 2022: the knowledge base for standardized bacterial and archaeal data	109
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids	108
Rhea, the reaction knowledgebase in 2022	108
UFold: fast and accurate RNA secondary structure prediction with deep learning	107
Bacteria have numerous distinctive groups of phage–plasmids with conserved phage and variable plasmid gene repertoires	106
Dynamics and competition of CRISPR–Cas9 ribonucleoproteins and AAV donor-mediated NHEJ, MMEJ and HDR editing	105
Recombination machinery engineering facilitates metabolic engineering of the industrial yeast Pichia pastoris	104
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins	104
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models	104
DM3Loc: multi-label mRNA subcellular localization prediction and analysis based on multi-head self-attention mechanism	103
InsectBase 2.0: a comprehensive gene resource for insects	102
Genome-wide mapping of G-quadruplex structures with CUT&Tag	101
GlycoPOST realizes FAIR principles for glycomics mass spectrometry data	100
Biological Magnetic Resonance Data Bank	100
Crystal structure of SARS-CoV-2 nsp10 bound to nsp14-ExoN domain reveals an exoribonuclease with both structural and functional integrity	98
Sequence- and structure-specific cytosine-5 mRNA methylation by NSUN6	97
RING 3.0: fast generation of probabilistic residue interaction networks from structural ensembles	96
G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders	95
SUMOylation of YTHDF2 promotes mRNA degradation and cancer progression by increasing its binding affinity with m6A-modified mRNAs	95
eggNOG 6.0: enabling comparative genomics across 12 535 organisms	95
catRAPIDomics v2.0: going deeper and wider in the prediction of protein–RNA interactions	95
GPCRdb in 2023: state-specific structure models using AlphaFold2 and new ligand resources	94
Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation	94
gutMGene: a comprehensive database for target genes of gut microbes and microbial metabolites	91
Diverse high-affinity DNA aptamers for wild-type and B.1.1.7 SARS-CoV-2 spike proteins from a pre-structured DNA library	91
Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations	91
CRISPR–Cas9 gRNA efficiency prediction: an overview of predictive tools and the role of deep learning	90
SCOPe: improvements to the structural classification of proteins – extended database to facilitate variant interpretation and machine learning	89
dbPTM in 2022: an updated database for exploring regulatory networks and functional associations of protein post-translational modifications	89
G-Quadruplexes as pathogenic drivers in neurodegenerative disorders	88
MirGeneDB 2.1: toward a complete sampling of all major animal phyla	88
Histone sumoylation and chromatin dynamics	87
miRTargetLink 2.0—interactive miRNA target gene and target pathway networks	87
SIRT3 consolidates heterochromatin and counteracts senescence	85
Reexamining assumptions about miRNA-guided gene silencing	85
Gramene 2021: harnessing the power of comparative genomics and pathways for plant research	85
SuperPred 3.0: drug classification and target prediction—a machine learning approach	84
TTD: Therapeutic Target Database describing target druggability information	84
Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter	84
PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions	83
eQuilibrator 3.0: a database solution for thermodynamic constant estimation	83
POSTAR3: an updated platform for exploring post-transcriptional regulation coordinated by RNA-binding proteins	83
EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure	83
HIT 2.0: an enhanced platform for Herbal Ingredients' Targets	82
A comprehensive epigenome atlas reveals DNA methylation regulating skeletal muscle development	82
AnimalTFDB 4.0: a comprehensive animal transcription factor database updated with variation and expression annotations	82
scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network	82
EMPIAR: the Electron Microscopy Public Image Archive	81
GraphBind: protein structural context embedded rules learned by hierarchical graph neural networks for recognizing nucleic-acid-binding residues	81
The N 6-methyladenosine RNA-binding protein YTHDF1 modulates the translation of TRAF6 to mediate the intestinal immune response	80
Argonaute integrated single-tube PCR system enables supersensitive detection of rare mutations	80
WashU Epigenome Browser update 2022	79
FireProtDB: database of manually curated protein stability data	79
PrankWeb 3: accelerated ligand-binding site predictions for experimental and modelled protein structures	79
canSAR: update to the cancer translational research and drug discovery knowledgebase	78
lncRNAfunc: a knowledgebase of lncRNA function in human cancer	78
KEA3: improved kinase enrichment analysis via data integration	78
miRNATissueAtlas2: an update to the human miRNA tissue atlas	78
Theoretical basis for stabilizing messenger RNA through secondary structure design	78
Power-law behavior of transcription factor dynamics at the single-molecule level implies a continuum affinity model	77
MobiDB: 10 years of intrinsically disordered proteins	77
OpenProt 2021: deeper functional annotation of the coding potential of eukaryotic genomes	77
The European Nucleotide Archive in 2021	76
Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome	76
CAMPR4: a database of natural and synthetic antimicrobial peptides	76
IPC 2.0: prediction of isoelectric point and pKa dissociation constants	76
Epitranscriptomic editing of the RNA N6-methyladenosine modification by dCasRx conjugated methyltransferase and demethylase	76
GenBank 2023 update	75
VARIDT 2.0: structural variability of drug transporter	75
OmicsNet 2.0: a web-based platform for multi-omics integration and network visual analytics	75
Staying true to yourself: mechanisms of DNA methylation maintenance in mammals	75
Structural basis for substrate recognition and cleavage by the dimerization-dependent CRISPR–Cas12f nuclease	75
DISCO: a database of Deeply Integrated human Single-Cell Omics data	74
MarkerDB: an online database of molecular biomarkers	73
DeepST: identifying spatial domains in spatial transcriptomics by deep learning	72
PADLOC: a web server for the identification of antiviral defence systems in microbial genomes	72
CRISPR/Cas13 effectors have differing extents of off-target effects that limit their utility in eukaryotic cells	72
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation	71
The European Genome-phenome Archive in 2021	71
Suppression of liquid–liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells	71
Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations	71
MetaboAnalyst 6.0: towards a unified platform for metabolomics data processing, analysis and interpretation	71
Genomic impact of stress-induced transposable element mobility in Arabidopsis	71