Some recent Molecular Biology Databases
| Database name | URL | Short description |
| 3′aQTL-atlas | https://wlcb.oit.uci.edu/3aQTLatlas | 3′UTR alternative polyadenylation quantitative trait loci |
| AlphaFold Protein Structure Database | https://alphafold.ebi.ac.uk | Protein structures predicted by AlphaFold |
| Animal-eRNAdb | http://gong_lab.hzau.edu.cn/Animal-eRNAdb | Animal enhancer RNAs |
| AMDB | http://leb.snu.ac.kr/amdb | Animal Microbiome Database |
| ASMdb | http://www.dna-asmdb.com | Allele-Specific DNA Methylation Database |
| ARTS-DB | https://arts-db.ziemertlab.com | Database for Antibiotic Resistant Targets |
| BrainBase | https://ngdc.cncb.ac.cn/brainbase | Brain disease knowledgebase |
| CancerMIRNome | http://bioinfo.jialab-ucr.org/CancerMIRNome | miRNA profiles in cancer |
| CancerSCEM | https://ngdc.cncb.ac.cn/cancerscem | Human cancer single-cell gene expression |
| CeDR | https://ngdc.cncb.ac.cn/cedr | Drug responses in health and disease from scRNA-seq |
| CircleBase | http://circlebase.maolab.org | Human extrachromosomal circular DNA |
| circMine | http://www.biomedical-web.com/circmine or http://hpcc.siat.ac.cn/circmine | Human circRNA transcriptome in health and disease |
| CompoDynamics | https://ngdc.cncb.ac.cn/compodynamics | Sequence composition and characteristics across genomes |
| ConVarT | https://convart.org | Orthologous variants between human, mouse and worm |
| CovPDB | http://www.pharmbioinf.uni-freiburg.de/covpdb | Covalent inhibitors and their complexes |
| CTR-DB | http://ctrdb.ncpsb.org.cn | Patient-derived clinical transcriptomes and drug responses |
| CyanoOmicsDB | http://www.cyanoomics.cn | Cyanobacteria genomics and transcriptomics |
| DDinter | http://ddinter.scbdd.com | Drug-drug interactions |
| DISCO | https://www.immunesinglecell.org | Deep Integration of Single-Cell Omics |
| dNTPpoolDB | https://dntppool.org | dNTP concentrations in vivo |
| EVA | https://www.ebi.ac.uk/eva | European Variation Archive |
| EWAS Open Platform | https://ngdc.cncb.ac.cn/ewas | Analysis platform for EWAS research |
| Gene Expression Nebulas | https://ngdc.cncb.ac.cn/gen | Expression profiles across species, bulk and single cell |
| GPEdit | https://hanlab.uth.edu/GPEdit | A-to-I RNA editing in cancer |
| GproteinDb | https://gproteindb.org | G proteins and their interactions |
| GRAND | https://grand.networkmedicine.org | Human gene regulation models |
| gutMGene | http://bio-annotation.cn/gutmgene | Target genes of gut microbes and microbial metabolites in human and mouse |
| huARdb | https://huarc.net/database | Human Antigen Receptor database |
| Human Proteoform Atlas | http://human-proteoform-atlas.org | Human proteoforms |
| INDI | http://research.naturalantibody.com/nanobodies | Integrated Nanobody Database for Immunoinformatics |
| qPTMplants | http://qptmplants.omicsbio.info | Plant PTMs, including quantitation |
| Kincore | http://dunbrack3.fccc.edu/kincore | Protein kinase sequence, structure and phylogeny |
| LIRBase | https://venyao.xyz/lirbase | Long Inverted Repeats in eukaryotes |
| lncRNAfunc | https://ccsm.uth.edu/lncRNAfunc | Regulatory roles of lncRNAs in cancer |
| m5C-Atlas | http://www.xjtlu.edu.cn/biologicalsciences/m5c-atlas | The 5-methylcytosine (m5C) epitranscriptome |
| mBodyMap | https://mbodymap.microbiome.cloud/#/mbodymap | Distribution of microbes across the human body in health and disease |
| MetazExp | http://bioinfo.njau.edu.cn/metaExp | Analysis of gene expression and alternative splicing in metazoans |
| miTED | http://microrna.gr/mited | microRNA Tissue Expression Database |
| msRepDB | https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html | multi-species Repeat DataBase |
| MVIP | https://mvip.whu.edu.cn | Multi-omics Portal of Viral Infection |
| Nanobase.org | https://nanobase.org | DNA, RNA or protein-DNA/RNA hybrid nanostructures |
| NCATS Inxight: Drugs | https://drugs.ncats.io | Drugs, their properties and regulation |
| NMDC Data Portal | https://data.microbiomedata.org | Multi-omics microbiome data |
| NPCDR | https://idrblab.org/npcdr or http://npcdr.idrblab.net | Drug-Natural Product combinations and diseases |
| NP-MRD | http://np-mrd.org | Natural Products Magnetic Resonance Database |
| OlfactionBase | https://olfab.iiita.ac.in/olfactionbase | Odors, Odorants and Olfactory Receptors |
| OncoDB | http://www.oncodb.org. | Gene Expression and Viral Infection in Cancer |
| ONQUADRO | http://onquadro.cs.put.poznan.pl | DNA and RNA quadruplexes |
| PCMDB | http://www.tobaccodb.org/pcmdb | Plant Cell Marker Database |
| PlantGSAD | http://systemsbiology.cau.edu.cn/PlantGSEAv2 | Plant gene set annotations |
| PncsHub | https://pncshub.erc.monash.edu | Non-classically secreted proteins in Gram-positive bacteria |
| Pol3Base | http://rna.sysu.edu.cn/pol3base/index.php | PolIII-transcribed ncRNAs |
| proCHiPdb | http://prochipdb.org | Chromatin immunoprecipitation database for prokaryotic organisms |
| PopHumanVar | https://pophumanvar.uab.cat | Causal variants of selective sweeps |
| ProNAB | https://web.iitm.ac.in/bioinfo2/pronab | Protein-Nucleic Acid Binding affinity |
| Regeneration Roadmap | https://ngdc.cncb.ac.cn/regeneration/index | Literature and multi-omics data on cell regeneration |
| R-loopBase | https://rloopbase.nju.edu.cn | R-loops and R-loop regulators |
| RNAPhaSep | http://www.rnaphasep.cn | RNAs involved in liquid-liquid phase separation |
| RPS | http://rps.renlab.org | RNAs involved in liquid-liquid phase separation |
| scAPAatlas | http://www.bioailab.com:3838/scAPAatlas | scRNAseq-based analysis of alternative polyadenylation across cells, tissues and species |
| scAPAdb | http://www.bmibig.cn/scAPAdb | scRNAseq-based analysis of alternative polyadenylation across cells, tissues and species |
| scEnhancer | http://enhanceratlas.net/scenhancer | Single-cell enhancer resource |
| scMethBank | https://ngdc.cncb.ac.cn/methbank/scm | Single Cell methylation data |
| SomaMutDB | https://vijglab.einsteinmed.org/SomaMutDB | Somatic mutations in normal human tissues |
| SPENCER | http://spencer.renlab.org | Cancer-associated ncRNA-encoded small peptides |
| SPICA | https://spica.unil.ch | Swiss Portal for Immune Cell Analysis |
| SYNBIP | https://idrblab.org/synbip | Synthetic binding proteins |
| TcoFBase | http://bio.liclab.net/TcoFbase | Transcription cofactors in human and mouse |
| TF-Marker | http://bio.liclab.net/TF-Marker | Human transcription factors, especially as cell markers |
| TISMO | http://tismo.cistrome.org | Mouse syngeneic tumor models |
| TissueNexus | https://www.diseaselinks.com/TissueNexus | Tissue or cell line functional gene networks |
| TransLnc | http://bio-bigdata.hrbmu.edu.cn/TransLnc | Coding potential of lncRNAs across tissues, including neoantigens |
| tsRFun | http://biomed.nscc-gz.cn/DB/tsRFun | tsRNA expression and networks |
| VannoPortal | http://mulinlab.org/vportal | Human genetic variants vs traits and diseases |
| VEuPathDB | http://VEuPathDB.org | Eukaryotic pathogens, their vectors and hosts |
| ViMIC | http://bmtongji.cn/ViMIC/index.php | Virus Mutations, Integration sites and Cis-effects |
| ViroidDB | https://viroids.org | Viroids and viroid-like circular RNA agents |
| VThunter | https://db.cngb.org/VThunter | scRNA-seq-based analysis of virus receptor expression across animals |
| webTWAS | http://www.webtwas.net | Transcriptome-Wide Association Studies |
| ZOVER | http://www.mgc.ac.cn/cgi-bin/ZOVER/main.cgi | Zoonotic and vector-borne viruses |