Tag: molecular biology

ChEMBL is a manually curated database of bioactive molecules with drug-like properties. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs.

The information in the database is presented at two levels: the initial view or landing pages for each target family provide expert-curated overviews of the key properties and selective ligands and tool compounds available. For selected targets more ...

Database that aims to advance understanding about how environmental exposures affect human health. It provides manually curated information about chemical–gene/protein interactions, chemical–disease and gene–disease relationships. These data are inte ...

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information.

The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules that serves a global community of researchers, educators, and students. The data contained in the archive include atomic ...

The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in ...

BioModels is a repository of computational models of biological processes. It allows users to search and retrieve mathematical models published in the literature. Many models are manually curated (to ensure reproducibility) and extensively cross-link ...

The Protein Data Bank in Europe (PDBe) is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. It is a founding member of the worldwide Protein Data Bank which collects, organises a ...

PharmGKB is a resource that provides information about how human genetic variation affects response to medications. PharmGKB collects, curates and disseminates knowledge about clinically actionable gene-drug associations and genotype-phenotype relati ...

The PeptideAtlas Project provides a publicly-accessible database of peptides identified in tandem mass spectrometry proteomics studies and software tools. Mass spectrometer output files are collected for human, mouse, yeast, and several other organis ...

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

The Database of Protein Disorder (DisProt) is a curated database that provides information about intrinsically disordered proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part. Disordered regions ...

Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...

A bioinformatic database of antimicrobial resistance genes, their products and associated phenotypes.

Europe PubMed Central (Europe PMC) is an on-line database that offers free access to a large and growing collection of biomedical research literature.

PrimerBank is a public resource for PCR primers. These primers are designed for gene expression detection or quantification (real-time PCR). PrimerBank contains over 306,800 primers covering most known human and mouse genes. There are several ways to ...

The Small Molecule Pathway Database (SMPDB) contains small molecule pathways found in humans, which are presented visually. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, ...

The Antimicrobial Peptide Database (APD) contains information on antimicrobial peptides from across a wide taxonomic range. It includes a glossary, nomenclature, classification, information search, prediction, design, and statistics of AMPs. The anti ...

The Protein Data Bank is the single worldwide archive of structural data of biological macromolecules.

The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

The Therapeutic Target Database provides information about therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links ...

Drug-related information: medical indications, adverse drug effects, drug metabolism and Gene Ontology terms of the target proteins.

SIDER contains information on marketed medicines and their recorded adverse drug reactions. The information is extracted from public documents and package inserts. The available information include side effect frequency, drug and side effect classifi ...

The Chemical Effects in Biological Systems (CEBS) database houses data of interest to environmental health scientists. CEBS is a public resource, and has received depositions of data from academic, industrial, and governmental laboratories.

The OpenNeuro project (formerly known as the OpenfMRI project) was established in 2010 to provide a resource for researchers interested in making their neuroimaging data openly available to the research community. It is managed by Russ Poldrack and C ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

This library is a public and easily accessible resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. The purpose of this database is to advance research on cellular ...

PubMed® comprises more than 30 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

CAMPR3 (Collection of Anti-Microbial Peptides) has been generated to enhance research into AMP families. The collection is compatible with well-known databases such as PubMed and Uniprot with information like sequence, protein definition, accession n ...

probeBase is a manually maintained and curated database of rRNA-targeted oligonucleotide probes and primers. Contextual information and multiple options for evaluating in silico hybridization performance against the most recent rRNA sequence database ...

SABIO-RK is a database for biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured.

The e-Mouse Atlas of Gene Expression (EMAGE) is a freely available database of in situ gene expression patterns that allows users to perform online queries of mouse developmental gene expression. EMAGE is unique in providing both text-based descripti ...

IMGT/PRIMER-DB is the IMGT® oligonucleotide (primer) database for the immunoglobulins (IG) and T cell receptors (TR). The IG and TR primers are useful for combinatorial library constructions, antibody single chain Fragment variable (scFv), phage dis ...

Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research a ...

IntEnz is a freely available resource focused on enzyme nomenclature. IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification ...

Open TG-GATEs is a public toxicogenomics database developed so that a wider community of researchers could utilize the fruits of TGP and TGP2 research. This database provides public access to data on 170 of the compounds catalogued in TG-GATEs. Data ...

Useful biological numbers

Toxin and Toxin Target Database (T3DB) is a bioinformatics resource that combines detailed toxin data with comprehensive toxin target information.

The GGBN Data Standard is a set of terms and controlled vocabularies designed to represent sample facts. It does not cover e.g., scientific name, geography, or physiological facts. This allows combining the GGBN Data Standard with other complementary ...

The Pancreatic Expression Database (PED) is a repository for pancreatic-derived -omics data. With a generic web-based system, the database provides the research community with an open access tool to mine currently available pancreatic cancer experime ...

BACTIBASE contains calculated or predicted physicochemical properties of bacteriocins produced by both Gram-positive and Gram-negative bacteria. The information in this database is very easy to extract and allows rapid prediction of relationships str ...

PDBe-KB (Protein Data Bank in Europe - Knowledge Base) is a community-driven resource managed by the PDBe team, collating functional annotations and predictions for structure data in the PDB archive. PDBe-KB is a collaborative effort between PDBe and ...

APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome ...

EpiFactors is a web-accessible database that provides broad information about human proteins and complexes involved in epigenetic regulation. It also lists corresponding genes and their expression levels in several samples, in particular 458 human pr ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

DrugCentral is online drug information that provides information on active ingredients, chemical entities, pharmaceutical products, drug mode of action, indications, and pharmacologic mode of action. DrugCentral monitors FDA, EMA, and PMDA for new dr ...

The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical ...

SureChEMBL is a publicly available large-scale resource containing compounds extracted from the full text, images and attachments of patent documents. The data are extracted from the patent literature according to an automated text and image-mining p ...

The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-li ...

This resource is a collection of all proteins identified to be localized on kinetochore, centrosome, midbody, telomere and spindle from two fungi (S. cerevisiae and S. pombe) and five animals, including C. elegans, D. melanogaster, X. laevis, M. musc ...

Herbal active Ingredients and their Targets

PseudoBase is a collection of RNA pseudoknots that have been made available for retrieval to the scientific community.

CellFinder maps validated gene and protein expression, phenotype and images related to cell types.The data allow characterization and comparison of cell types and can be browsed by using the body browser and by searching for cells or genes. All cells ...

T-psi-C is a database of tRNA sequences and 3D tRNA structures. The T-psi-C database can be continuously updated by any member of the scientific community.

HyperCLDB is the hypertext on cell culture availability built from the Cell Line Data Base of the Interlab Project. As for February 2017 it features 6,643 lines, 6,301 of which are available for distribution. From these, 4,921 are human cell lines (1 ...

Three-dimensional Electron Microscopy (3DEM) has become a key experimental method in structural biology for a broad spectrum of biological specimens from molecules to cells. The EMDataResource project provides a unified portal for deposition, retriev ...

IPPI-DB is a database of modulators of protein-protein interactions. It contains exclusively small molecules and therefore no peptides. The data are retrieved from the literature either peer reviewed scientific articles or world patents. A large vari ...

Protein-protein and drug-protein interactions for studies of drug repositioning

FerrDb is a manually curated resource for regulators and markers of ferroptosis and ferroptosis-disease associations.

Antiviral peptides (AVPs) have exhibited huge potential in inhibiting viruses by targeting various stages of their life cycle. Therefore, we have developed AVPdb, available online at http://crdd.osdd.net/servers/avpdb, to provide a dedicated resource ...

WITHDRAWN is a database of withdrawn and discontinued drugs that were recalled from global markets due to safety concerns. The database serves as a useful resource with information about the therapeutic (or primary) targets, off-targets, toxicity typ ...

CentrosomeDB is a collection of human and drosophila centrosomal genes that were reported in the literature and other sources. The database offers the possibility to study the evolution, function, and structure of the centrosome. They have compiled i ...

Oligonucleotides for targeted resequencing of the human genome

This database contains information on microbial biocatalytic reactions and biodegradation pathways for primarily xenobiotic, chemical compounds. The goal of the EAWAG-BBD is to provide information on microbial enzyme-catalyzed reactions that are impo ...

Antihypertensive peptides database

Biomarkers of exposure to disease risk factors

REFOLDdb is a resource for the optimization of protein refolding, referring to published methods employed in the refolding of recombinant proteins. It stores a collection of published experimental approaches and records for refolding proteins. It con ...

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) is an open-access, comprehensive database containing information on amino acid sequences, chemical modifications, 3D structures, bioactivities and toxicities of peptides that p ...

An integrated database of ncRNA interactions. Noncoding RNAs (ncRNAs) play crucial regulatory roles in a variety of biological circuits. To document regulatory interactions between ncRNAs and biomolecules, we previously created the NPInter database ...

Drug2Gene is a free multi-species drug-target knowledge base. It contains integrated and unified data of publicly available relations between drugs/compounds and their gene/protein targets gathered from 20 publicly available bio- and chemoinformatics ...

A resource for computational drug design and discovery

The Gemina system (http://gemina.igs.umaryland.edu) identifies, standardizes and integrates the outbreak metadata for the breadth of NIAID category A–C viral and bacterial pathogens (http://www3.niaid.nih.gov/biodefense/PDF/cat.pdf), thereby p ...

A collection of molecular interaction maps and pathways involved in cancer development and progression with a focus on melanoma.

Experimentally validated Cell Penetrating Peptides

Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator cu ...

DNAzymes i.e. DNA molecules with catalytic activity

Disco Cross Docking Benchmark server for automated pose and ranking prediction of ligand binding.

G-quadruplex Ligands Database

Dual RNA-seq host-pathogen sequencing

A database of high-resolution MS/MS spectra for lichen metabolites. The Global Natural Product Social Molecular Networking (GNPS) site creates a community for natural product researchers working with mass spectrometry data. MassIVE Datasets : Docum ...

A chemical data resource with relational data between natural products and biological sources. NPBS Database of Shanghai Institute of Organic Chemistry.

FuncPEP is a database of functional peptides encoded by non-coding RNAs.

a comprehensive database of RNAs associated with drug sensitivity from multi-omics data. RNAactDrug a comprehensive database of RNAs associated with Drug sensitivity from multi-omics data. RNAactDrug is a comprehensive resource for querying associa ...

Drug-peptide conjugates

BiPOm is an ontology based on systemic representation of metabolic processes. BiPOm is an ontological model carrying the main biological processes and molecular roles/functions at a high level of genericity where the usual annotated resources are tre ...

The FoldamerDB is an open source database of foldamers. Foldamers are molecules which mimics the folding of biological molecules into well defined conformation

Database for ncRNA expression in human extracellular vesicles.

A comprehensive portal of HLA-peptide interactions affected by SARS-CoV-2 mutations.

Database for skin permeation of xenobiotics. Jupyter Notebook which leads through the code used to create huskinDB publication Figures. huskinDB is a human skin permeation database containing information on experimental protocols used. It provides ...

A database of molecular replacements for ligand design

A database of structurally annotated peptides

World Data Center of Microorganisms collections

Nutritional and medicinal value of plant-based foods

The 5' and 3' untranslated regions of eukaryotic mRNAs may play a crucial role in the regulation of gene expression controlling mRNA localization, stability and translational efficiency. For this reason we developed UTRdb, a specialized database of 5 ...

A comprehensive knowledge of all the factors involved in splicing, both proteins and RNAs, and of their interaction network is crucial for reaching a better understanding of this process and its functions. A large part of relevant information is buri ...

The Standard European Vector Architecture: a platform for analysis of complex prokaryotic phenotypes

A database of gene transcription regulatory networks

DNA vectors and data for genetic manipulation of malaria parasites

Traditional Chinese Medicine Integrated Database

Vaccine Investigation and Online Information Network

ChemHub is a comprehensive database for selecting biosynthetic target molecules based on compound functions.

Pangenomic sets of microarray probes for organisms with fully sequenced genomes

Natural compounds and their suppliers

Mechanisms of antimicrobial resistance

Adverse Drug Reaction Classification System

Heterogenous data on unstudied and understudied drug targets

Essential Host Factors for Pathogenic Infection

Biologically relevant ligand-protein interactions

Naturally occuring Plant based Anticancerous Compound Targets

Biotransformation of xenobioitics - drugs and food ingredients - by human enzymes

Genomics of Drug Sensitivity in Cancer: Sensitivity for anti-cancer drugs in various cell lines

MitopatHs is a database that allows to navigate among the biochemical pathways (PatHs) of human (H) mitochondria (Mito). It is a logically-framed tool for visualizing multiple mitochondrial pathways.

Potential drug-binding sites in protein structures from the PDB

Genes and proteins involved in human and yeast cell cycle

A collection of functional sequence patterns located in UTR sequences.

Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the s ...

The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly de ...

RNA editing database in organelles.

A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

>>>!!!<<< Data originally published in the JCB DataViewer has been moved BioStudies. Please note that while the majority of data were moved, some authors opted to remove their data completely. >>>!!!<<< Migrated data can be found at https://ww ...

Helmholtz Repository of Bioparts (HeRBi) provides plasmids to the scientific community, delocalised within the different Helmholtz centers.

VirOligo is a database of virus-specific oligonucleotides. VirOligo contains PCR primers and hybridization probes used for detection of viral nucleic acids and the experimental conditions used in their detection. The latter include temperature regime ...

PathCards is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more h ...

A database for facilitating the search for drug adverse reaction target. It contains information about known drug adverse rection targets, functions and properties. Associated references are also included.

ZINC Express is a virtual assistant for purchasing compounds annotated in the ZINC Database.

The Molecular Probe Data Base (MPDB) was set up in 1992 with the objective of allowing researchers to retrieve information on molecular probes and synthetic oligonucleotides that had proven useful in real experimental conditions. MPDB includes inform ...

WormBook (http://www.wormbook.org) is an open-access, online collection of original, peer-reviewed chapters on the biology of C. elegans and related nematodes. It contains over 100 chapters, covering nearly every aspect of C. elegans research, from c ...

>>>!!!<<< 2021-08; The repository is no longer available. >>>!!!<<< Archived page of Taenia solium genome project see https://web.archive.org/web/20160309194611/http://www.taeniasolium.unam.mx/taenia

The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle gen ...

>>>>!!<<< As detected 2017-11-24 TBNet India is no longer accessible >>>>!!<<<< TBNet India is an initiative by the Department of Biotechnology, Govt of India with special focus on Indian contributions on research and various issues related to tuber ...

qPrimerDepot is a primer database for RT-PCR analysis of greater than 99% of human and mouse RefSeq genes. These primers sets are designed to be used under uniform annealing temperatures to facilitate their application in large scale high throughput ...

The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis. We present both raw (sequences, structure models, metadata) and processed (analyses, evolution ...

Web based application designed to integrate protein structure, protein sequence and protein annotations in a unique graphical environment. The current version of the application offers a unified, enriched and interactive view of EMDB volumes, PDB str ...

----<<<<< This repository is no longer available. This record is out dated >>>>>----- The aim of FlyReactome, based in the Department of Genetics, University of Cambridge, is to develop a curated repository for Drosophila melanogaster pathways ...

The Peptaibol Database is a sequence and structure resource for the unusual class of peptides known as peptaibols. The database includes sequence, biological source, and bibliographical data for the naturally-occurring peptaibols. Information is also ...

A database that collects tetrads, quadruplexes, and G4-helices found in PDB-deposited structures of nucleic acids. It stores their sequences, secondary and tertiary structures, and motif-specific description including planarity, rise and twist parame ...

The defensins knowledgebase is a manually curated database and information source devoted to the defensin family of antimicrobial peptides. The current version of the database holds a comprehensive collection of over 350 defensin records each contain ...

The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data port ...

METLIN represents the largest MS/MS collection of data with the database generated at multiple collision energies and in positive and negative ionization modes. The data is generated on multiple instrument types including SCIEX, Agilent, Bruker and W ...

NeuroCirc is an integrative web-based resource of circRNA expression in the human brain, which allows interactive exploration of circRNA expression across multiple datatsets, including circRNA expression in bulk brain tissue, circQTLs, circRNA expres ...

COlleCtion of Open Natural prodUcTs (COCONUT): an aggregated dataset of elucidated and predicted NPs collected from open sources and a web interface to browse, search and easily and quickly download ntural products (NPs). NPs are small molecules prod ...

LOTUS (naturaL prOducTs occUrrence databaSe) is one of the biggest and best annotated resources for NPs occurrences available free of charge and without any restriction. Natural Products Online is an open source project for Natural Products (NPs) sto ...

The database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. For selection purposes and for correlation of structural similarity with medical application, the assignment of the Anatomical Therapeutic Chemi ...

Bacterial sRNAs are a class of small regulatory RNAs of about 40 – 500 nt in length, and play a variety of important roles in many biological processes through binding to their target mRNAs or proteins. With the application of high-throughput seque ...

Drug repositioning, the process of discovering, validating, and marketing previously approved drugs for new indications, is of growing interest to academia and industry due to reduced time and costs associated with repositioned drugs. Computational m ...

Antibiotic resistance has become a major human health concern due to widespread use, misuse and overuse of antibiotics. In addition to antibiotics, antibacterial biocides and metals can contribute to the development and maintenance of antibiotic resi ...

The Host Genetic and Immune Factors Shaping Human Microbiota (GIMICA) is a database systematically providing host genetic factors (HGFs) and host immune factors (HIFs). Both factors are essential for defining the chemical and physical landscapes inha ...

The Variability of Drug Transporter Database (VARIDT) is constructed to provide the comprehensive data of all aspects of drug transporter variability. Based on the comprehensive review on all FDA approved and >2,000 clinical trial drugs, VARIDT confi ...

The Interactome of Drug-Metabolizing Enzymes (INTEDE) is a database designed to systematically provide the data of all types of drug-metabolizing enzyme (DME) interaction. INTEDE confirmed 1,047 unique DMEs (448 host and 599 microbial), for the first ...

Complete Genomics provides free public access to a variety of whole human genome data sets generated from Complete Genomics’ sequencing service. The research community can explore and familiarize themselves with the quality of these data sets, review ...

CoDNaS-RNA is a database of the Conformational Diversity in the Native State of RNA molecules. Each entry in CoDNaS-RNA is a redundant collection of known structures of the same RNA molecule, which can be considered as alternative instances of the RN ...

The HIV Drug Resistance Database is a compilation of mutations in HIV genes that confer resistance to anti-HIV drugs. Currently, 673 mutations to RT, Protease, Env, Gag, Integrase, FIV RT and SIV RT are stored. The database may be searched by gene, c ...

Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals). These replication domains replicate in a stable, cell type-specific temporal order during S-phase that is closely linked to their 3 ...

To bridge the gap between the rising information needs of biological and medical researchers and the rapidly growing number of online bioinformatics resources, we have created the Online Bioinformatics Resources Collection (OBRC) at the Health Scienc ...

G-protein coupled receptors (GPCRs) represent one of the most important families of drug targets in pharmaceutical development. GLIDA is a novel public GPCR-related chemical genomic database that is primarily focused on the correlation of information ...

The StrainInfo.net Bioportal currently integrates data from 55 Biological Resource Centres (BRCs) that cover all earth's continents and range from small niche-specific research collections to large general-purpose service collections into an integrat ...