Some More Molecular Biology Databases

Aging Atlas 

https://bigd.big.ac.cn/aging 

Aging related omics data 

Animal-APAdb 

http://gong_lab.hzau.edu.cn/Animal-APAdb/ 

Alternative polyadenylation in animals 

AcrDB 

http://bcb.unl.edu/AcrDB/ 

Anti-CRISPR operons 

AcrHub 

http://pacrispr.erc.monash.edu/AcrHub 

Anti-CRISPR proteins 

ATACdb 

http://www.licpathway.net/ATACdb 

Human Assay-for-Transposase-Accessible Chromatin data 

AtMAD 

http://www.megabionet.org/atmad 

Arabidopsis thaliana Multi-omics Association Database 

BastionHub 

http://bastionhub.erc.monash.edu/ 

Substrates of Gram-negative secretion systems 

BiG-FAM 

https://bigfam.bioinformatics.nl 

Biosynthetic gene cluster families 

CancerImmunityQTL 

http://www.cancerimmunityqtl-hust.com/ 

ImmunQTLs across multiple cancer types 

Chewie-NS 

https://chewbbaca.online/ 

Gene-by-gene schemas for microbial strain identification 

CMNPD 

https://www.cmnpd.org/ 

Comprehensive Marine Natural Product Database 

CNCDatabase 

https://cncdatabase.med.cornell.edu/ 

Cancer drivers at non-coding regions 

cncRNAdb 

http://www.rna-society.org/cncrnadb/ 

Coding and non-coding RNA 

ConjuPepDB 

http://conjupepdb.ttk.hu/ 

Drug-peptide conjugates 

CovInDB 

http://cadd.zju.edu.cn/cidb/ 

Covalent Inhibitor DataBase 

crisprSQL 

http://www.crisprsql.com/ 

CRISPR/Cas9 Off-Target Cleavage Assays 

CRISPR-view 

http://crispviewdatabase.weililab.org/ 

Functional genetic screens 

CSEA-DB 

https://bioinfo.uth.edu/CSEADB/ 

Cell type specificity of genetic traits 

CSVS 

http://csvs.babelomics.org/ 

Spanish genomes and exomes 

Cyanorak 

http://www.sb-roscoff.fr/cyanorak 

Comparative genomics of cyanobacteria 

Datanator 

https://datanator.info/ 

Molecular data for modeling biochemical networks 

dbCAN-PUL 

http://bcb.unl.edu/dbCAN_PUL/home 

Experimentally characterized CAZyme gene clusters 

dbGuide 

https://sgrnascorer.cancer.gov/dbguide 

Manually curated and functionally validated guide RNAs 

DescribePROT 

http://biomine.cs.vcu.edu/servers/DESCRIBEPROT/ 

Residue level prediction of structure and function across proteomes 

DKK 

https://darkkinome.org/ 

Dark Kinome Knowledgebase 

DIGGER 

https://exbio.wzw.tum.de/digger 

Alternative splicing and protein-protein interactions 

DNAmoreDB 

http://www.genesilico.pl/DNAmoreDB 

DNAzymes, i.e. DNA molecules with catalytic activity 

DrugSpaceX 

https://drugspacex.simm.ac.cn/ 

100 million compounds for virtual screening 

DualSeqDB 

http://www.tartaglialab.com/dualseq/ 

Dual RNA-seq host-pathogen sequencing 

FireProtDB 

https://loschmidt.chemi.muni.cz/fireprotdb 

Protein stability data 

gcType 

http://gctype.wdcm.org/ 

WDCM 10K sequencing projects 

GIMICA 

https://idrblab.org/gimica/ 

Host Genetic and Immune Factors Shaping Human Microbiota 

GlycoPOST 

https://glycopost.glycosmos.org/ 

Raw Mass Spectrometry glycomics data 

GRNdb 

http://www.grndb.com/ 

TF-target relationships inferred from single cell and bulk RNA-seq datasets 

GSRS 

https://gsrs.ncats.nih.gov/app/substances 

Global Substance Registration System 

HeRA 

https://hanlab.uth.edu/HeRA/ 

Human enhancer RNA Atlas 

HERB 

http://herb.ac.cn/ 

High-throughput Experiment- and Reference-guided dataBase of TCM 

Housekeeping Transcript Atlas 

http://www.housekeeping.unicamp.br/ 

Human and mouse housekeeping genes 

HumanMetagenomeDB 

https://webapp.ufz.de/hmgdb/ 

Curated and standardized metadata for human metagenomes 

iCSDB 

http://www.kobic.re.kr/icsdb 

integrated CRISPR Screens DataBase 

IDDB 

http://mdl.shsmu.edu.cn/IDDB 

Infertility Disease DataBase 

iModulonDB 

https://imodulondb.org/ 

‘iModulons’, groups of independently-modulated genes 

IndiGenomes 

http://clingen.igib.res.in/indigen/ 

Genetic variation in 1000 Indian individuals 

INTEDE 

https://idrblab.org/intede/ 

Interactome of Drug-Metabolizing Enzymes 

KinaseMD 

https://bioinfo.uth.edu/kmd/ 

Kinase Mutations and Drug responses 

LnCeCell 

http://bio-bigdata.hrbmu.edu.cn/LnCeCell/ 

lncRNA-associated ceRNA networks 

LncExpDB 

https://bigd.big.ac.cn/lncexpdb 

Human lncRNA expression database 

LncSEA 

http://bio.liclab.net/LncSEA/ 

Reference human lncRNA sets 

m6A-Atlas 

http://www.xjtlu.edu.cn/biologicalsciences/atlas 

The N6-methyladenosine (m6A) epitranscriptome including base-resolution data 

markerDB 

http://www.markerdb.ca/ 

Biomarkers: chemical, protein, chromosomal and genetic 

MASI 

http://www.aiddlab.com/MASI/ 

Microbiota – Active Substance Interactions database 

MeDAS 

https://das.chenlulab.com 

Alternative splicing during development in 20 species 

MemMoRF 

http://memmorf.hegelab.org 

Membrane-binding Molecular Recognition Features 

mMGE 

http://mgedb.comp-sysbio.org/ 

Human metagenomic extrachromosomal mobile genetic elements 

MolluscDB 

http://mgb.biocloud.net/home 

Comparative genomics of molluscs 

Nucleome Data Bank 

https://ndb.rice.edu/ 

3D genome structures and simulations 

OncoVar 

https://oncovar.org/ 

Driver mutations, genes and pathways in cancer 

Open Targets Genetics 

https://genetics.opentargets.org/ 

Drug targets prioritised from genetic data 

PCAT 

http://pedtranscriptome.org 

Pediatric cancer transcriptome explorer 

Peryton 

https://dianalab.e-ce.uth.gr/peryton 

Microbe–disease associations 

PheLiGe 

https://phelige.com/ 

Genotype–phenotype associations 

PhycoCosm 

http://phycocosm.jgi.doe.gov/ 

Comparative genomics of algae 

PK-DB 

https://pk-db.com/ 

Pharmacokinetics data from clinical trials and pre-clinical research 

Planet Microbe 

https://www.planetmicrobe.org/ 

Oceanographic omics datasets linked to environmental metadata 

Plant-ImputeDB 

http://gong_lab.hzau.edu.cn/Plant_imputeDB 

Reference panels and imputation methods for plant genomes 

PROTAC-DB 

http://cadd.zju.edu.cn/protacdb/ 

Proteolysis-targeting chimeras (PROTACs) 

RASP 

http://rasp.zhanglab.net/ 

RNA secondary structure probing data 

RBP2GO 

https://rbp2go.dkfz.de 

RNA-binding proteins across species 

RJunBase 

www.RJunBase.org 

RNA splice junctions 

RMDisease 

http://www.xjtlu.edu.cn/biologicalsciences/rmd 

Genetic variants that affect RNA modifications vs disease 

RMVar 

http://rmvar.renlab.org 

Genetic variants that affect RNA modifications vs disease 

SC2disease 

http://easybioai.com/sc2disease/ 

Single cell transcriptomics data and disease 

SilencerDB 

http://health.tsinghua.edu.cn/silencerdb or http://bioinfo.au.tsinghua.edu.cn/silencerdb/ 

Human silencers, validated or predicted 

STAB 

http://stab.comp-sysbio.org/ 

Spatio-Temporal Cell Atlas of the Human Brain 

TBDB 

https://tbdb.io 

Structurally annotated T-box riboswitch: tRNA pairs 

TCRdb 

http://bioinfo.life.hust.edu.cn/TCRdb 

T-cell receptor (TCR) sequences 

ThermoMutDB 

http://biosig.unimelb.edu.au/thermomutdb 

Protein Mutation Thermodynamics Database 

TISCH 

http://tisch.comp-genomics.org/ 

Uniformly processed tumor (and microenvironment) scRNA-seq data 

TransCirc 

https://www.biosino.org/transcirc/ 

Protein coding potential of circRNAs 

tRFtarget 

http://trftarget.net 

Targets of tRNA-derived fragments 

tsRBase 

http://tsrbase.org/ 

tRNA-derived small RNA expression and function 

VARAdb 

http://www.licpathway.net/VARAdb/ 

Variants and regulatory information