List of Molecular Biology Databases 2023

Molecular Biology Databases 2023

Database name	URL	Short description
ABC Portal	http://abc.sklehabc.com	Single cell transcriptomics of blood cells
AgeAnno	https://relab.xidian.edu.cn/AgeAnno/#/	Single cell annotation of aging in human
Amylograph	http://AmyloGraph.com/	Amyloid-amyloid interactions
Animal-SNPAtlas	http://gong_lab.hzau.edu.cn/Animal_SNPAtlas/	High-quality SNPs in 20 animal species
Antibody Registry	https://antibodyregistry.org	Antibodies, their antigens and catalogue numbers
Aquila	https://aquila.cheunglab.org	Spatial omics data
ASCancer Atlase	https://ngdc.cncb.ac.cn/ascancer/home	Alternative splicing in cancer
BIC	http://bic.jhlab.tw/	Bacteria in Cancer
Brain Catalog	https://ngdc.cncb.ac.cn/braincatalog	Genetics of brain disorders and related phenotypes
BV-BRC	https://www.bv-brc.org/	Bacterial and Viral Bioinformatics Resource Center
CEDAR	https://cedar.iedb.org/	Cancer Epitope Database and Analysis Resource
Cell Taxonomy	https://ngdc.cncb.ac.cn/celltaxonomy	Cell types and markers across species, tissues and conditions
Cell Tracer	http://bio-bigdata.hrbmu.edu.cn/CellTracer	Multi-omics of cellular development trajectories
ChemFOnt	https://www.chemfont.ca	Chemical Functional Ontology
ChemPert	https://chempert.uni.lu/	Transcriptomics responses to pertubagens in non-cancerous cells
CMDB	https://db.cngb.org/cmdb/	Whole-genome sequencing data of 141,000 Chinese individuals
ChromLoops	https://3dgenomics.hzau.edu.cn/chromloops	Protein-mediated chromatin loops
CohesinDB	https://cohesindb.iqb.u-tokyo.ac.jp	Multi-omics data on cohesin functions
COMBATdb	https://db.combat.ox.ac.uk	COVID-19 Multi-omics Blood Atlas
CottonMD	http://yanglab.hzau.edu.cn/CottonMD/	Multi-omics data on cotton
CovInter	https://idrblab.org/covinter	Interactions between coronavirus RNAs and host proteins
CRAMdb	http://www.ehbio.com/CRAMdb	Microbiome metagenomes across animals
CRdb	http://cr.liclab.net/crdb/	Human chromatin regulators
CREAMMIST	https://creammist.mtms.dev	Cancer drug dose-reponse across cell lines
CRISPRbase	http://crisprbase.maolab.org	CRISPR Base Editing
DirectRMDB	http://www.rnamd.org/directRMDB/	RNA modifications from direct RNA sequencing
DRESIS	https://idrblab.org/dresis/	Drug resistance
DrugMAP	https://idrblab.org/drugmap/	Molecular Atlas and Pharma-information of drugs
DupScan	https://dupscan.sysumeg.com/	Vertebrate genome duplications
EDomics	http://edomics.qnlm.ac	Comparative multi-omics for animal Evo-Devo
EmAtlas	http://bioinfor.imu.edu.cn/ematlas	Spatiotemporal multi-omics of mammalian embryogenesis
FAVOR	https://favor.genohub.org	Functional Annotation of Variants – Online Resource
Fungal Names	https://nmdc.cn/fungalnames/	Fungal taxonomy
G4Atlas	https://www.g4atlas.org/	Experimentally determined RNA G-quadruplexes in transcriptomes
GAIA	https://gaia.cobius.usherbrooke.ca	Predicted G-quadruplexes in genomes and transcriptomes
GenomicKB	https://gkb.dcmb.med.umich.edu/	Knowledge Graph for the Human Genome
GotEnzymes	https://metabolicatlas.org/gotenzymes	Predicted enzyme kinetic parameters
GPSAdb	https://www.gpsadb.com/	Genetic Perturbation Similarity Analysis
HGD	https://ngdc.cncb.ac.cn/hgd	Homolog Gene Database – expression, traits, variants across species
HiChIPdb	http://health.tsinghua.edu.cn/hichipdb/	HiChIP regulatory interactions
HProteome-BSite	https://galaxy.seoklab.org/hproteome-bsite/database	Predicted binding sites and ligands in the human 3D proteome
HTCA	https://www.htcatlas.org	Single cell transcriptomes and analytical tools
HUSCH	http://husch.comp-genomics.org	Human Universal Single Cell Hub
IAnimal	https://ianimal.pro/	Multi-omics data for 21 animals
ipaQTL	http://bioinfo.szbl.ac.cn/iaQTL/	Intronic polyadenylation quantitative trait loci
IEAtlas	http://bio-bigdata.hrbmu.edu.cn/IEAtlas	HLA-presented immune epitopes from non-coding regions etc
ImmCluster	http://bio-bigdata.hrbmu.edu.cn/ImmCluster	Immunology cell types in normal and cancer tissues
IntroVerse	https://rytenlab.com/browser/app/introverse	Introns and splicing errors/noise
isomiRdb	https://anathema.cs.uni-saarland.de/isomirdb/	microRNA isoform expression
Lineage Landscape	http://data.iscr.ac.cn/lineage/#/home	Omics of lineage determination in animals
M6AREG	https://idrblab.org/m6areg/	m6A vs disease and drug response
MeDBA	https://medba.ddtmlab.org	Metalloenzyme families, structures, ligands
MediaDive	https://mediadive.dsmz.de	Culture media
MHC Motif Atlas	http://mhcmotifatlas.org/	MHC Binding Specificities and Ligands
microbioTA	http://bio-annotation.cn/microbiota	Cancer microbiomes
MiMeDB	https://mimedb.org	Human-microbe interactions and their metabolomes
NACDDB	https://genesilico.pl/nacddb/	Nucleic Acid Circular Dichroism Database
NEMO Archive	https://nemoarchive.org	Neuroscience Multi-Omic Archive
NLRscape	https://nlrscape.biochim.ro/	Plant Nod-like receptors
OrganoidDB	http://www.inbirg.com/organoid_db/	Organoid transcriptomics
PAT	http://bioinfo.qd.sdu.edu.cn/PAT/	Prokaryotic Antimicrobial Toxin database
PDCM Finder	www.cancermodels.org	Patient-Derived Cancer Models
PGG.MHC	https://pog.fudan.edu.cn/pggmhc	Population genetics of HLA genes
PGG.SV	https://www.biosino.org/pggsv	Human genome structural variants
PertOrg	http://www.inbirg.com/pertorg/	Changes induced in model organisms by in vivo genetic perturbation
plantEXP	https://biotec.njau.edu.cn/plantExp	Plant gene (co-)expression and alternative splicing
ProPan	https://ngdc.cncb.ac.cn/propan	Prokaryotic pan-genomes
ProtCAD	http://dunbrack2.fccc.edu/protcad	Protein Common Assembly Database
qPTM	http://qptm.omicsbio.info	Quantitative Post-Translational Modifications
QUADRAtlas	https://rg4db.cibio.unitn.it	RNA G-Quadruplex and RG4-binding proteins
RABC	http://www.onethird-lab.com/RABC/	Multi-omics of Rheumatoid Arthritis
RBPimage	http://rnabiology.ircm.qc.ca/RBPImage/	Microscopy reporting subcellular distribution of human RNA binding proteins
Ribocentre	https://www.ribocentre.org	Ribozymes
RiboXYZ	https://ribosome.xyz	Ribosome structures
Ribo_uORF	http://rnainformatics.org.cn/RiboUORF	uORFs from ribosome profiling data
RLBase	https://gccri.bishop-lab.uthscsa.edu/shiny/rlbase/	R-loops in the human genome
RM2Target	http://rm2target.canceromics.org/	Targets of RNA modification proteins
SPASCER	https://ccsm.uth.edu/SPASCER	Spatial transcriptomics annotation at single-cell resolution
SPEED	http://speedatlas.net	Single-cell pan-species atlas
SUMMER	http://njmu-edu.cn:3838/SUMMER/	Biomarkers, GWAS and cancer survival
tatDB	https://grigoriev-lab.camden.rutgers.edu/tatdb	Experimentally supported targets of tRNA-derived fragments
TEDD	https://TEDD.obg.cuhk.edu.hk/	Temporal Expression of Development Database
TFSyntax	https://tfsyntax.zhaopage.com	Transcription Factor binding syntax
Thing Metabolome Repository family	http://metabolites.in/things	LC–MS metabolomics data
TIMEDB	https://timedb.deepomics.org	RNAseq data and the tumor immune micro-environment
TmAlphaFold	https://tmalphafold.ttk.hu/	AlphaFold TM protein predictions, membrane-embedded and assessed
tModBase	https://www.tmodbase.com/	tRNA modifications: enzymes, dynamics, diseases
TOXRIC	http://toxric.bioinforai.tech/	Toxicological data and benchmarks
TWAS Atlas	https://ngdc.cncb.ac.cn/twas/	Transcriptome-wide association studies
UFCG	https://ufcg.steineggerlab.com	Fungal core genes

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Table 2.

Updated descriptions of databases most recently published elsewhere

Database name	URL	Short description
Chemical Probes Portal	https://www.chemicalprobes.org/	Chemical probe assessment and selection
CIViC	https://civicdb.org/	Clinical interpretation of variants in cancer
EMPIAR	https://empiar.org/	The Electron Microscopy Public Image Archive
EpiFactors	http://epifactors.autosome.org	Human epigenetic factors and complexes
FerrDb	http://www.zhounan.org/ferrdb/	Ferroptosis regulators
SulfAtlas	https://sulfatlas.sb-roscoff.fr/	Sulfatase families