Tag: proteomics

Universal Protein resource. A database of protein sequence and functional information, many entries being derived from genome sequencing projects. It contains a large amount of information about the biological function of proteins derived from the re ...

STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations.

The Human Protein Atlas is program started with the aim to map of all the human proteins in cells, tissues and organs using integration of various omics technologies. It consists of three parts: Tissue Atlas showing the distribution of proteins acros ...

The PRIDE PRoteomics IDEntifications database is a centralized, standards compliant, public data repository that provides protein and peptide identifications together with supporting evidence.

The SWISS-MODEL Repository is a database of annotated 3D protein structure models generated by the SWISS-MODEL homology-modelling pipeline for protein sequences of selected model organisms.

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 ...

The Immunology Database and Analysis Portal (ImmPort) data repository was created for the exploration of clinical and basic research data on immunology and associated findings. ImmPort intends to promote effective data sharing across the basic, clini ...

The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in ...

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 ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination.

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

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 ...

ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interacti ...

MassIVE is a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data. MassIVE datasets can be assigned ProteomeXchange accessions to satisfy publication ...

ProteomicsDB is a protein-centric in-memory database for the exploration of large collections of quantitative mass spectrometry-based proteomics data. ProteomicsDB was first released in 2014 to enable the interactive exploration of the first draft of ...

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 BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

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

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, su ...

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

jPOSTrepo (Japan ProteOme STandard Repository) is a data repository of sharing MS raw/processed data.

neXtProt is a comprehensive human-centric discovery platform, offering its users a seamless integration of and navigation through protein-related data.

The Protein Circular Dichroism Data Bank (PCDDB) is an open-access online repository for protein circular dichroism spectral- and meta-data. Users may freely extract and deposit validated data and the validation process is conveniently integrated int ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

The Termini-Oriented Protein Function INferred Database (TopFIND) is an integrated knowledgebase focused on protein termini, their formation by proteases and functional implications. It contains information about the processing and the processing sta ...

MitoMiner is an integrated data warehouse of mammalian localisation evidence, phenotypes and diseases. This data has been integrated to allow the creation of sophisticated data mining queries spanning many different sources. It is primarily concerned ...

PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images ...

The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources, including both open and controlled access data resources. The resource ...

Network of database and computational resources including KEGG (pathways, interactions, etc.) and DBGET/LinkDB (an integrated database retrieval system). It also hosts several web-based tools for sequence analysis (i.e. Blast, Motif, Clustal W).

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

The LINCS Data Portal provides a unified interface for searching LINCS dataset packages and reagents. LINCS data are being made openly available as a community resource through a series of data releases, so as to enable scientists to address a broad ...

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

Arabidopsis Protein Phosphorylation Site Database

iProX is a public platform for collecting and sharing raw data, analysis results and metadata obtained from proteomics experiments. The iProX repository employs a web-based proteome data submission process and open sharing of mass spectrometry-based ...

Function: Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules. The analysis is based on coefficient tables deduced from the published literature.

DEPOD - the human DEPhOsphorylation Database is a manually curated database collecting human active and inactive phosphatases, their experimentally verified protein and non-protein substrates, and dephosphorylation site information, and pathways in w ...

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

HumanCyc is a bioinformatics database that describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional ...

Phosphorylation sites in various species identified by mass spectrometry

PlanMine is an integrated web resource of data & tools to mine Planarian biology.

LOCATE is a curated database that houses data describing the membrane organization and subcellular localization of proteins from the RIKEN FANTOM4 mouse and human protein sequence set.

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

The SugarBind Database (SugarBindDB) was created in 2002 as part of an effort by the MITRE Corporation (http://www.mitre.org) to develop a pathogen-capture technology based on the binding of viral, bacterial and biotoxin lectins to specific glycans ( ...

MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Tricho ...

The ApiDB website (http://eupathdb.org/eupathdb) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center that integrates numerous database resources. The phylum Apicomplexa comprises numerous veterinary and med ...

Global survey of organ and organelle protein expression in mouse: combined proteomic and transcriptomic profiling. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tis ...

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

Proteome-pI is an online database containing information about predicted isoelectric points for 5,029 proteomes (21 million of sequences) calculated using 18 methods. The isoelectric point, the pH at which a particular molecule carries no net electri ...

ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents

Unimod is a community-supported, comprehensive database of protein modifications for mass spectrometry applications. The aim is to provide accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by all ...

COVDB contains cell culture, animal model, and clinical data on compounds with a proven or potential anti-coronavirus activity.

Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and aids identification of potential cell surface diagnostic markers, drug targets, or vaccine components. PSORTdb comprises ePSORTdb, a manual ...

The aim of PEROXISOME database (PeroxisomeDB) is to gather, organise and integrate curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders.

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

Developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a c ...

The compendium of crop Proteins with Annotated Locations (cropPAL) collates more than 550 data sets from previously published fluorescent tagging or mass spectrometry studies and eight pre-computed subcellular predictions for barley, wheat, rice and ...

NASA GeneLab expands scientists’ access to experiments that explore the molecular response of terrestrial biology to spaceflight environments. The vast amounts of raw data generated by experiments aboard the International Space Station are being made ...

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 ...

The dbDEPC is a database of differentially expressed proteins in human cancers.

CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

GlycoPOST is a mass spectrometry data repository for glycomics. Users can release their "raw/processed" data via this site with a unique identifier number for the paper publication. Submission conditions are in accordance with the Minimum Information ...

An integrated Omics data warehouse for Locust, Locusta migratoria

EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

Web resource designed to provide a central repository for the storage and the analysis of data on domain peptide recognition obtained with interaction assays exploiting peptide chip technology.

Regulatory Network in Protein Phosphorylation

The AlloMAPS database provides data on the energetics of communication in proteins with well-documented allosteric regulation, allosteric signalling in PDBselect chains, and allosteric effects of mutations. In addition to energetics of allosteric sig ...

CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biologic ...

RepetDB provides repeat consensus detected and classified by TEdenovo and used by TEannot to annotate copies in genomes.

An InterMine interface to data from Phytozome

XenMine has been created to view, search and analyze Xenopus data, and provides essential information on gene expression changes and regulatory elements present in the genome. It contains published genomic datasets from both Xenopus tropicalis and Xe ...

RNArchitecture is a database that provides a comprehensive description of relationships between known families of structured ncRNAs, with focus on sequence and structure similarities. RNArchitecture also provides literature information and links to o ...

A database of curated biomolecular interactions.

DIGGER is an essential resource for studying the mechanistic consequences of alternative splicing such as isoform-specific interaction and consequence of exon skipping. The database integrates information of domain-domain and protein-protein interact ...

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats. ProRepeat collects repeats from all proteins included in the UniProt knowledgebase, together wit ...

Aging related omics data

Arabidopsis thaliana Protein Interactome Database

EuRBPDB is a comprehensive and user-friendly database for classifying and annotating eukaryotic RNA binding proteins (RBPs) drawn from various public databases. Over 100 eukaryotic species such as human, mouse, fly, worm and yeast are included. EuRBP ...

The ECM-protein knowledge database. Please follow MatrisomeDB. MatrisomeDB will be hosted at matrisomedb.org very soon.

PhaSepDB is a novel database that provides a collection of phase separation related proteins manually curated from publications and public database. In addition to curated proteins, PhaSepDB also provides the researchers with molecular signatures th ...

It is a unique comparative genomics database from plant-genome-based proteome data sets. Evolutionarily conserved motifs were extracted by MEME software from protein-sequence annotation groups selected by BLASTP from the proteome data sets of 10 spec ...

The Dynamic Proteomics database is a compendium of endogenously YFP-tagged human proteins and their time-lapse microscopy movies. These movies show the protein dynamics in space and in time in individual living human cancer cells in response to an an ...

A public standards-compliant repository for gel-based proteomics data linked to protein identification published in the literature. The repository is continuously extended, putting together a large collection of multi-species reference maps, with tho ...

A resource for computational drug design and discovery

A data resource of liquid-liquid phase separation in eukaryotes. Here, we presented a data resource of LLPS (DrLLPS), a comprehensive data resource that contained 437,887 known and computationally detected LLPS-associated proteins in 164 eukaryotic ...

GELBANK is a publicly available database of two-dimensional gel electrophoresis (2DE) gel images of proteomes from organisms with known genome information (available at http://gelbank.anl.gov). GELBANK serves as a database for those proteomics labs t ...

Interacting and non-interacting protein pairs

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 ...

DescribePROT is a database containing annotations of 13 putative structural and functional properties at the amino acid level for ~1.4 million proteins from 83 popular/model organism, to be extended to hundreds of additional organisms. Users can sear ...

Database of molecular-level putative protein-drug interactions in the structural human proteome.

World-wide gel-based proteomics database.

Proteomic signature library of Staphylococcus aureus Pathophysiology for inter-experimental expression data analyses.

MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.

PeanutMine integrates peanut data from LIS PeanutBase and other sources.

This mine integrates many types of data for string bean built from the LIS chado database.

GrapeMine is dedicated to grapevine data. It provides access to many kind of data types like genomic annotation data as well as SNPs, markers and phenotyping data.

CowpeaMine integrates genomic and genetic data for cowpea, Vigna unguiculata. It is built from the LIS tripal.chado database as well as data from publications.

This mine integrates many types of data for soybean. It is currently under development by LIS, built from the LIS chado database (genomic data) and the SoyBase database (genetic data) as well as other resources

WheatMine integrates many types of data for Triticum aestivum including gene model, markers, and scaffolds. You can run flexible queries, export results and analyse lists of data.

ChickpeaMine integrates data for chickpea varieties desi and kabuli. It is developed by LIS/NCGR, built from the LIS chado database and the Chickpea Transcriptome Atlas - I.

This mine integrates data for multiple legume species. It is under development by NCGR and is built from the LIS and PeanutBase chado databases as well as exports from other sources.

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.

The National Population Health Data Center (NPHDC) is one of the 20 national science data center approved by the Ministry of Science and Technology and the Ministry of Finance. The Population Health Data Archive (PHDA) is developed by NPHDC relying o ...

A community resource of quantitative mass spectrometry-based proteomics datasets. MassIVE.quant is an extension of the Mass Spectrometry Interactive Virtual Environment (MassIVE) to provide the opportunity for large-scale deposition of data from qua ...

This tool is for understanding the coronavirus proteome and evaluating possible drug targets.

DIPPER is a spatiotemporal proteomics atlas of human intervertebral discs for exploring ageing and degeneration dynamics.

EPSD (Eukaryotic Phosphorylation Sites Database) is a well-annotated data resource of protein phosphorylation sites in eukaryotes.

a database for protein-peptide identification based on a hybrid clustering algorithm. PROPEDIA is a database of peptide-protein complexes clusterized in three methodologies: (i) peptide sequences; (ii) structure interface; and (iii) binding sites. P ...

Curated Protein Aggregation Database (CPAD) is an integrated database which contains information related to amyloidogenic proteins, Aggregation prone regions, aggregation kinetics and structure of proteins relevant to aggregation. Authors are encoura ...

A genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. An on-line source for Mycobacterium abscessus modeled structural proteome. MabeLLINI ...

dbPTM is a databases which accumulates the biological information related to protein post-translational modification (PTM), such as the catalytic sites, structural information, solvent accessibility of residues, protein secondary structures, protein ...

an annotated database of protein associations. Tabloid Proteome is a database of protein association network generated using publically available mass spectrometry based experiments in PRIDE.These associations represent a broad scala of biological a ...

CycloBranch is an open and platform-free software that provide the de novo generation of molecular formulas of unknown compounds in both liquid chromatography/mass spectrometry and mass spectrometry imaging datafiles.

DBAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method on genomic and proteomic data.

The UniProt archive (UniParc), part of the UniProt databases, is an archival protein sequence collection from all major publicly accessible resources. New and revised protein sequences are added daily into UniParc while not deleting the previous vers ...

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

Multi-omics knowledge database for cytomegaloviruses.

CuAS is an integrated database for Cucumber Alternative Splicing, includes genomic annotation, isoform-level functions, isoform-level features and tissue-specific AS events among multiple tissues.

2DE-pattern is a database containing data on proteins/isoforms/proteoforms profiles.

An authentic learning approach to teaching cancer genomics. On this site you can both (a) make and upload, and (b) download and analyse simulated patient case studies.

Explore Protein-Protein Interactions for Cancer Target Discovery Using the OncoPPi Portal. Translating Genomics Data into Protein-Protein Interaction Networks for Therapeutic Manipulation. This site provides a platform to facilitate discovery of ne ...

Samples and data for following disorders: Alzheimer's ,Cerebrovascular ,Degenerative brain disorder ,Fit and well, Glioma ,Meningitis ,Multiple sclerosis ,Progressive sclerosing poliodystrophy and others. Full list in Description… BRAIN UK is a virtu ...

A Comprehensive Resource for Targeted Proteomics Assays in the Community.

The Abalomics community portal is a community driven project to increase genetic knowledge of the abalone species.

How to Illuminate the Dark Proteome Using the Multi-omic OpenProt Resource. OpenProt is the first database that enforces a polycistronic model of eukaryotic genome annotations. Thus, OpenProt annotates known proteins (called RefProts) but also novel ...

The database of pre-computed isoelectric points and molecular weights for proteins and digest peptides from model organism's proteomes. Contains data for over 61 million protein sequences from 20,115 proteomes with isoelectric point predicted using 2 ...

A manually curated database of genomics, transcriptomics, proteomics and drug information for interstitial lung diseases. ILDGDB is a manually curated database that provides comprehensive experimentally supported associations between genes and inter ...

An integrative database of quantitative post-translational modifications in plants.

New Platform for the Analysis of the Molecular Impact of SARS-CoV-2 Viral Infection.

A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain.

A comprehensive resource for proteome-wide known and predicted ubiquitin ligase/deubiquitinase-substrate interactions in eukaryotic species.

Database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale.

DeepMitoDB is a database of experimental and predicted subcellular localization of mitochondrial proteins with exteded functional annotation.

AlphaKnot is a server that measures entanglement in AlphaFold-solved protein models while considering pLDDT confidence values.

FermFooDb is a database of peptides derived from fermented foods contains 2325 entries of unique peptides from the fermented foods.

Comprehensive database of Escherichia coli RNA-binding proteins (RBPs). This database documents RBPs identified by genome-wide survey of all known complete E. coli proteomes. EcRBPome also presents a cross-strain comparative account of these RBPs, as ...

A manually curated database of polycystic ovarian syndrome. Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein, PCOSBase: a manually curated database of polycystic ovarian syndrome, Datab ...

The One-stop Database for COVID-19 Specific Humoral Immunity and Clinical Parameters.

A database for alternative splicing atlas in livestock animals. The alternative splicing in livestock animals database (ASlive.org) is a collection of alternative splicing events across tissues in livestock animal speceis in including cattle (Bos ta ...

Enabling systems immunology with a manually curated intercellular immune interaction network. ImmunoGlobe is a map of the immune network that describes how different parts of the immune system work together to drive immune responses. By structuring ...

An Expertized Knowledge Database for the Model Legume Medicago truncatula. Medicago truncatula was proposed, about three decades ago, as a model legume to study the Rhizobium-legume symbiosis. It has now been adopted to study a wide range of biologi ...

DBSAV database reports GTS scores of human genes and DeepSAV scores of SAVs in the human proteome, including pathogenic SAVs, benign SAVs, gnomAD SAVs observed in exome sequencing, and all possible SAVs by single nucleotide variations. Each human pro ...

SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.

The National Omics Data Encyclopedia (NODE) is big data library with complete and integrative data storage, safe and efficiency-guaranteed data management as well as comprehensive and user-friendly data service functions. NODE stores raw sequence dat ...

The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyze and visualize primary in ...

The SWISS-2DPAGE database has been established in 1993 and is maintained collaboratively by the Central Clinical Chemistry Laboratory of the Geneva University Hopital and the Swiss Institute of Bioinformatics (SIB). The current release (Octobre, 2003 ...

The publicly available Proteome Database System for Microbial Research 2D-PAGE has been established at the Max Planck Institute for Infection Biology and serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. The ...

Data portal for the processing, analyzing, sharing and disseminating of metagenomic data sets

Huanglongbing (HLB) is a tritrophic disease complex involving citrus host trees, the Asian citrus psyllid (ACP) insect and a phloem restricted, bacterial pathogen Candidatus Liberibacter asiaticus (CLas). HLB is considered to be the most devastating ...

Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among ...

The UCLEB consortium of highly-phenotyped population-based prospective cohort studies provides a multi-omics data source consisting of genomics, metabolomics and proteomics for researching the molecular basis of disease and to inform drug development ...

The INTERVAL bioresource comprises 50,000 English blood donors, on whom deep molecular phenotypes (e.g. genomics, proteomics, metabolomics, lipidomics) have been generated. In over 100 years of blood donation practice, INTERVAL is the first randomise ...

The Fenland Study is a population-based cohort study of the interaction between environment and genetic factors in determining obesity, insulin sensitivity and hyperglycemia.

The EPIC Norfolk study is a population-based prospective cohort study. EPIC-Norfolk is part of the European Prospective Investigation of Cancer (EPIC), a large multi-centre cohort study with participants enrolled from 23 centres across Europe

DNMSO is an ontology for representing de novo sequencing results from Tandem-MS data. For the identification and sequencing of proteins, mass spectrometry (MS) has become the tool of choice and as such drives proteomics.

A repository of protein interaction data from mass spectrometry experiments.

A lims system to automate and expedite proteomics data management, processing and analysis.

An updated database for PTM dynamics in human, mouse, rat and yeast.

Deep Proteome Profiling Enabled Functional Annotation and Data-Independent Quantification of Proline Hydroxylation Targets.

Repository and statistical tools for directly determined PTM crosstalk based on long peptides measured by mass spectrometry. Focus on histone proteins.

CEDAR (The ComplexomE profiling DAta Resource) facilitates the storage and sharing of complexome profiling data, compliant with the MIACE standard , with the goal to enable and simplify their reuse.

Quercus robur annotation database

virusMS is a database for synthetic peptides of viruses with mass spectrometry. It is a tool for resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies.

Aeschynomene evenia genomic data from the Legume Information System

A user-friendly proteome database search software with an emphasis on deciphering the spectra of O-linked glycopeptides.

PICEAdatabase is a web database for Picea omics and phenotypic information.

An integrated Omics data warehouse for FAW, Spodoptera frugiperda

Database of plant protein inter-cultivar variability and function.

An integrated data warehouse for MaizeGDB

White and narrow-leaf lupin data from the Legume Information System

PaIntDB (Pseudomonas aeruginosa Interactions Database) is a tool for network-based omics integration and visualization using protein–protein interactions in Pseudomonas aeruginosa. PaIntDB contains more than 150K protein-protein (PPI) and protein-met ...

A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The datab ...

Protein-gene Expression Nexus (PEN), which consolidates an extensive dataset of paired proteomics and genomics studies. PEN present a database that allows researchers to easily and extensively visualize and annotate changes such as somatic copy numbe ...

An integrated omics database for functional genomic analysis of cyanobacteria.

A subcellular localisation database for Arabidopsis proteins, with online search interface.

A manually curated and comprehensive knowledge base for myocardial infarction.

This is the Schizosaccharomyces japonicus genome database.

A database for the molecular weight and isoelectric points of the plant proteomes.

An Open-source Platform for Hosting, Visualizing and Analyzing Protein Interaction Data.

A database of potential ligand binding sites in the human proteome.

A database of biomarkers of cancer stem cells.

Statistical detection of pathogen-associated protein domains.

An integrative platform to navigate the biology, structure and chemical inhibition of human proteins.

A genetic and proteomic database for the SARS-CoV, MERS-CoV, and SARS-COV-2.

GeneMANI helps you predict the function of your favourite genes and gene sets. GeneMania, a real-time multiple association network integration algorithm for predicting gene function.

A manually curated resource for multi-omics level evidence integration of fibrosis research

ExVe is the knowledge base of orthologous proteins identified in fungal extracellular vesicles.

DisEnrich—the database of human proteome IDRs that are significantly enriched in particular amino acids.

MyTardis began at Monash University to solve the problem of users needing to store large datasets and share them with collaborators online. Its particular focus is on integration with scientific instruments, instrument facilities and research lab fil ...

A Database of Experimentally Identified O-GlcNAc Sites and Proteins.

A Database of Host-Pathogen Protein-Protein Interactions and Annotation Features of the Bacteria Causing Huanglongbing HLB Disease.

Quickomics is a tool for exploring omics data in an intuitive, interactive and informative manner.

BoMiProt is a manually curated, comprehensive repository of published information of bovine milk proteins.

A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1.

A Database of Alfalfa-Bacterial Stem Blight Protein-Protein Interactions Revealing the Molecular Features of the Disease-causing Bacteria.

Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone.

Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures.

A project that's aim is to translate the human proteome into molecular and digital tools for drug discovery, personalized medicine and life science research. It offers a repository of synthesized peptides and different tools for analyzing them.

A comprehensive database for human proteome repeats. Human Proteome Repeats Database. HPREP : HUMAN PROTEOME REPEATS.

Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free en ...

The Contraceptive and Infertility Target DataBase. The CITDBase is a tool that provides a gateway for reproductive tissue-specific genes and proteins for research and the discovery of new contraceptive/infertility targets.

A Genome-wide Positioning Systems Platform to Catalyze Multi-omics for Alzheimer’s Therapeutic Discovery. A Network-based multi-omics analysis informs Alzheimer's patient care and therapeutic development.

>>>!!<<<This is an archive of the old NEBC site from nebc.nerc.ac.uk and is no longer updated. For new information regarding NERC Environmental Omics and the Bio-Linux system please see the EOS site at http://environmentalomics.org. >>>!!!<<< ...

A3D Database is a database for structure-based protein aggregation predictions for the human proteome

A machine learning-based phosphorylation sites prediction tool for Plasmodium proteins.

The One-stop Database for COVID-19-specific Antibody Responses and Clinical Parameters.

The Animal Proteome Database (AniProtDB) is a comprehensive collection of proteomes from 100 species spanning 21 animal phyla. In addition to providing open access to this collection of high-quality metazoan proteomes, information on predicted protei ...

VenomZone is a free web resource that provides information on venoms from six animal taxa (snakes, scorpions, spiders, cone snails, sea anemones and insects), as well as on their targets. Information can be browsed through pages on taxonomy, activity ...

Ebolabase is a comprehensive source for ebola-human interactions has been developed. Ebolabase contains experimentally verified entries of ebola-human interactions. The interactions are visualized as network images. This study provides the informatio ...

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

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 ...

The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metab ...

A Functional Analysis Tools for Post-translational Modifications (FAT-PTM) database, which supports data from publicly available proteomic analyses encompassing eight different types of PTMs and over 49,000 PTM sites.

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 ...

FABRIC Cancer Portal is a comprehensive catalogue of human coding genes in cancer based on the FABRIC framework. FABRIC quantifies the selection of genes in tumor and weighs their evidence for being cancer drivers.

<<<!!!<<< This repository is no longer available. >>>!!!>>> The main objective of our work is to understand the pathomechanisms of late onset neurodegenerative disorders such as Huntington's, Parkinson's, Alzheimer's and Machado Joseph disease and to ...

SWATHAtlas is a repository of mass spectrometry data of the human proteome. The repository provides open access to libraries of SWATH-MS (Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra) datasets. SWATH-MS is a method whi ...

The BIONDA biomarker database provides structured information on all biomarker candidates published in PubMed articles. There is no limitation to any kind of diseases. To this end, PubMed article abstracts and renowned databases such as UniProt and H ...

<<<!!!<<< This repository is no longer available. >>>!!!>>> A human interactome map. The sequencing of the human genome has provided a surprisingly small number of genes, indicating that the complex organization of life is not reflected in the gene ...

>>>!!!!<<< Retirement of UniProt Metagenomic and Environmental Sequences (UniMES): UniProt has retired UniMES as there is now a resource at the EBI that is dedicated to serving metagenomic researchers. Henceforth, we recommend using the EBI Metagen ...

Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies. The METATRYP software consists of:. METATRYP allows users to investigate the occurrence of tryptic peptides within the protein coding sequen ...

A database of exclusive proteins from Leishmania parasite. Leishmania Exclusive Protein Database. The Leishmania Exclusive Protein database (Leish-ExP) is a repository of protein sequences specific to five Leishmania species and genus. Leishmania i ...

>>>!!!<<< OMICtools is no longer online >>>!!!<<< We founded OMICtools in 2012 with the vision to drive progress in life science. We wanted to empower life science practitioners all over the world to achieve breakthroughs by getting data to talk. W ...