The Electron Microscopy Data Bank (EMDB) is a public repository for cryogenic-sample Electron Microscopy (cryoEM) volumes and representative tomograms of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, helical reconstruction, electron tomography, subtomogram averaging, and electron crystallography (for more information, see the EMDB Policies). 

Biotechnology and Biological Sciences Research Council

AMED

NBDC

Ministry of Electronics and Information Technology

National Institute of General Medical Sciences

Unified Data Resource for Large Complexes Determined by Cryo-Electron Microscopy

The BMRB as an evolving resource for biomolecular structure-function research

National Institute of Allergy and Infectious Diseases

National Cancer Institute

PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS

National Science Foundation

U.S. Department of Energy

Wellcome Trust

Data Discovery Engine

PubTator

synthetic construct

Escherichia coli

Severe acute respiratory syndrome coronavirus 2

Saccharomyces cerevisiae

Human immunodeficiency virus 1

Bioimaging

Electron Microscopy

Atomic Resolution X-Ray Crystallography

Tomography

Electron Microscopy Data Bank

Fairsharing.org

Homo sapiens

Mus musculus

Bos taurus

Rattus norvegicus

Oryctolagus cuniculus

Conditions of use

Conformation

Molecular Mass

Resolution

WormBase is an international consortium of biologists and computer scientists providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematodes. Founded in 2000, the WormBase Consortium is led by Paul Sternberg (CalTech), Matt Berriman (The Wellcome Trust Sanger Institute), Sarah Dyer (EBI), and Lincoln Stein (The Ontario Institute for Cancer Research). WormBase is a founding member of the Alliance of Genome Resources Project.

National Human Genome Research Institute

WormBase: a core data resource for C. elegans and other nematodes

UK Medical Research Council

Biothings API

filarial elephantiasis

Onchocerciasis

Caenorhabditis elegans

Caenorhabditis brenneri

Caenorhabditis japonica

Caenorhabditis remanei

Pristionchus pacificus

Brugia malayi

Onchocerca volvulus

Strongyloides ratti

Trichuris muris

Annotation

RNAi knockdown assay

Curation

WormBase

re3data.org

Gene Function

Phenotype

"The Human Immunology Project Consortium (HIPC) program was established in 2010, and renewed in 2015 and in 2022, by the NIAID Division of Allergy, Immunology, and Transplantation as part of the overall NIAID focus on human immunology. Through this program, well-characterized human cohorts are studied using a variety of modern analytic tools, including multiplex transcriptional, cytokine, and proteomic assays; multiparameter phenotyping of leukocyte subsets; assessment of leukocyte functional status; and multiple computational methods. 

Through the HIPC program, centralized research resources and a comprehensive, centralized database will be constructed for use by the greater scientific community. The information gained from the HIPC program will provide a comprehensive understanding of the human immune system and its regulation and will reveal novel associations between components of the immune system and other biological systems, identify novel immune mediators and pathways, establish predictors of vaccine safety in different populations, and enable the rapid evaluation of different vaccine formulations and administration regimens in human populations. This knowledge base will also serve as a foundation for the future study of immune-mediated diseases in the human, such as allergy, asthma, transplant rejection, autoimmune diseases, and a variety of inflammatory diseases."

HIPC Data Coordinating Center

Drug Hypersensitivity

Asthma

autoimmune disease

Flow Cytometry

Mass Cytometry

Mass Spectrometry

transcription profiling assay

ImmuneSpace

ALEdb (i) is a web-based platform that comprehensively reports on ALE acquired mutations and their conditions, (ii) reports key mutations using previously established trends, (iii) enables a search-driven workflow to enhance user mutation functional analysis through mutation cross-reference, (iv) allows exporting of mutation query results for custom analysis, (v) includes a bibliome describing the databased experiment publications and (vi) contains experimental evolution mutations from multiple model organisms.

ALEdb is freely available for non-commercial use. It is hosted and maintained by the Systems Biology Research Group at the University of California, San Diego. The PI and Group leader for the ALE activities at UCSD is Dr. Adam Feist. If you are interested in contributing to it or have general questions about its use, please email, afeist@ucsd.edu. 

Systems Biology Approach to Redefine Susceptibility Testing and Treatment of MDR Pathogens in the Context of Host Immunity

Novo Nordisk Foundation

Center for Biosustainability

Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)

Escherichia coli (strain B / REL606)

Escherichia coli str. K-12 substr. MG1655

Escherichia coli BW25113

RNA-seq assay

population growth assay

Microbial Culture Procedure

ALEdb

integbio.jp

Database Commons

genetic variation

growth condition

population measurement

The aim of the FlyBase project is to provide an openly accessible centralized resource for Drosophila genetic, genomic and functional data. It  is carried out by a consortium of Drosophila researchers and computer scientists at: Harvard University, University of Cambridge (UK), Indiana University and the University of New Mexico.

FlyBase: A Drosophila Genomic and Genetic Database

Alliance Central: A platform for sustainable development of next generation genome knowledgebases

National Institute of Diabetes and Digestive and Kidney Diseases

Investigating metabolic responses to high sugar diets and the onset of diabetic phenotypes

FlyBase

Drosophila melanogaster

The Database of Antimicrobial Activity and Structure of Peptides (DBAASP) has been created to provide users with detailed information on experimentally tested peptides regarding their chemical structure and activity against specific targets. The database is manually curated and contains information on ribosomal, nonribosomal, and synthetic peptides that show antimicrobial activity as Monomers, Multimers, and Multi-Peptides.

disease by infectious agent

bacterium

Fungi

Minimum Inhibitory Concentration Test

cytotoxicity assay

3D structure prediction

Database of Antimicrobial Activity and Structure of Peptides

Viruses

Hemolysis

cytotoxicity measurement

Peptide Conformation

The Hepatitis C Virus (HCV) Database Project was initially funded by the Division of Microbiology and Infectious Diseases of the National Institute of Allergies and Infectious Diseases (NIAID). The HCV database group strives to present HCV-associated, hand-annotated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools.

This project is deeply indebted to the HIV Database Group, led by Dr. Bette Korber, for much of its tools, infrastructure and philosophy; the two databases continue to collaborate closely and to share software and resources.

To our users Please note that the HCV database site is no longer funded by NIH. We try to keep the database updated and the tools running, but we cannot guarantee we can quickly resolve problems.

Los Alamos National Laboratory

Hepacivirus hominis

sequence alignment

data transformation

Hepatitis C Virus Database Project (HCV)

Gene Feature

Phylogenetics

Geographic Distribution

The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins, with accurate, consistent and rich annotation. In addition to capturing the core data mandatory for each UniProtKB entry (mainly, the amino acid sequence, protein name or description, taxonomic data and citation information), as much annotation information as possible is added. This includes widely accepted biological ontologies, classifications and cross-references, and clear indications of the quality of annotation in the form of evidence attribution of experimental and computational data. The UniProt Knowledgebase consists of two sections: a reviewed section containing manually-annotated records with information extracted from literature and curator-evaluated computational analysis (aka "UniProtKB/Swiss-Prot"), and an unreviewed section with computationally analyzed records that await full manual annotation (aka "UniProtKB/TrEMBL").

European Molecular Biology Laboratory

Alzheimer's Research UK

State Secretariat for Education, Research and Innovation

PRO: A Protein Ontology in Open Biomedical Ontologies

National Library of Medicine

Linking Text Mining and Data Mining for Biomedical Knowledge Discovery

Delaware INBRE

and the National Science Foundation

National Eye Institute

National Heart Lung and Blood Institute

National Institute of Mental Health

UniProt: A centralized protein sequence and function resource

UniProt

EcoCyc captures information from 44,000 publications for Escherichia coli K-12 substr. MG1655. Use EcoCyc to search for knowledge on E. coli genes, regulation, and metabolism; analyze transcriptomics data; perform comparative analyses; and run a metabolic model.

National Center for Research Resources

The EcoCyc Model Organism Database for Escherichia coli

Genome assembly

Sequence Analysis

EcoCyc

Re3data.org

ITN TrialShare shares information about ITN's clinical studies and specimen bio-repository. Data and analysis code underlying ITN-published manuscripts are publicly available with the goal of promoting transparency, reproducibility, and scientific collaboration.

Immune Tolerance Network

cytometry assay

flow cytometry assay

Immune Tolerance Network TrialShare Clinical Trials Research Portal

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