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Found 312 result(s)

European Chemical Biology Database

ECBD

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The European Chemical Biology Database (ECBD) is a prototype database, currently being developed for EU-OPENSCREEN. The purpose of ECBD is to store and integrate screening data from EU-OPENSCREEN partners and contributors.

Screening Unit Berlin-Buch

Screening Unit Jens Peter von Kries

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The mission of the platform is to enable access for academic projects towards experiments in high-throughput without loss of IP and on a cost basis, which does not restrict access towards HTS usage. The FMP hosts the central open access technology platform of EU-OPENSCREEN, the ChemBioNet and theHelmholtz-Initiative für Wirkstoffforschung, the Screening Unit. The Unit serves for systematic screening of large compound or genome-wide RNAi libraries with state-of-the-art equipment like automated microscopes and microfluidic systems. The Screening Unit is part of the Chemical Biology Platform of the FMP also supported by the MDC. See also: https://www.mdc-berlin.de/screening-unit

OceanColor web

Ocean Biology DAAC

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The Ocean Biology Processing Group (OBPG) serves as the Distributed Active Archive Center (DAAC) for all Ocean Biology (OB) data produced or collected under NASA’s Earth Observing System Data and Information System (EOSDIS). This website thus serves as the primary data access portal to the NASA OB.DAAC. The links below provide a variety of methods to access the holdings of the OB.DAAC, including visual browsers that enable point-and-click access by data levels and direct access for bulk download. In agreement with partner organizations, some data access requires user registration to enable better tracking of usage metrics.

PDBj

Protein Data Bank Japan

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PDBj (Protein Data Bank Japan) provides a centralized PDB archive of macromolecular structures, integrated tools for data retrieval, visualization, and functional characterization. PDBj is supported by JST-NBDC and Osaka University.

SISSA Open Data

Scuola Internazionale Superiore di Studi Avanzati Open Data

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SISSA Open Data is the Sissa repository for the research data managment. It is an institutional repository that captures, stores, preserves, and redistributes the data of the SISSA scientific community in digital form. SISSA Open Data is managed by the SISSA Library as a service to the SISSA scientific community.

Smithsonian Research Online

SRO

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The Smithsonian Repository is a digital service that collects, preserves, and disseminates research materials via several communities including Research Data Sets. It preserves and protects the organization's legacy...

MetabolomeXchange

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MetabolomeXchange.org delivers the mechanisms needed for disseminating the data to the metabolomics community at large (both metabolomics researchers and databases). The main objective is to make it easier for metabolomics researchers to become aware of newly released, publicly available, metabolomics datasets that may be useful for their research. MetabolomeXchange contains datasets from different data providers: MetaboLights, Metabolomic Repository Bordeaux, Metabolomics Workbench, and Metabolonote

Mechanism and Catalytic Site Atlas

CSA (formerly)

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M-CSA is a database of enzyme reaction mechanisms. It provides annotation on the protein, catalytic residues, cofactors, and the reaction mechanisms of hundreds of enzymes. There are two kinds of entries in M-CSA. 'Detailed mechanism' entries are more complete and show the individual chemical steps of the mechanism as schemes with electron flow arrows. 'Catalytic Site' entries annotate the catalytic residues necessary for the reaction, but do not show the mechanism. The M-CSA (Mechanism and Catalytic Site Atlas) represents a unified resource that combines the data in both MACiE and the CSA

Protein Circular Dichroism Data Bank

PCDDB

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The Protein Circular Dichroism Data Bank (PCDDB) provides and accepts a circular dichroism spectra data. The PCDDB and it's parent organization, the Institute of Structural and Molecular Biology (ISMB), investigate molecular structure using techniques such as biomolecular nuclear magnetic resonance, X-ray crystallography and computational structure prediction, as methods for protein production and biological characterization.

SABIO-RK

System for the Analysis of Biochemical Pathways - Reaction Kinetics

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The SABIO-RK is a web-based application based on the SABIO relational database that contains information about biochemical reactions, their kinetic equations with their parameters, and the experimental conditions under which these parameters were measured. It aims to support modellers in the setting-up of models of biochemical networks, but it is also useful for experimentalists or researchers with interest in biochemical reactions and their kinetics. All the data are manually curated and annotated by biological experts, supported by automated consistency checks.

Comparative RNA Web

CRW

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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, accuracy) data, organized into four main sections.

ChEMBL

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ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.

EMDataResource

formerly: EMDataBank

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Cryo electron microscopy enables the determination of 3D structures of macromolecular complexes and cells from 2 to 100 Å resolution. EMDataResource is the unified global portal for one-stop deposition and retrieval of 3DEM density maps, atomic models and associated metadata, and is a joint effort among investigators of the Stanford/SLAC CryoEM Facility and the Research Collaboratory for Structural Bioinformatics (RCSB) at Rutgers, in collaboration with the EMDB team at the European Bioinformatics Institute. EMDataResource also serves as a resource for news, events, software tools, data standards, and validation methods for the 3DEM community. The major goal of the EMDataResource project in the current funding period is to work with the 3DEM community to (1) establish data-validation methods that can be used in the process of structure determination, (2) define the key indicators of a well-determined structure that should accompany every deposition, and (3) implement appropriate validation procedures for maps and map-derived models into a 3DEM validation pipeline.

Chemical Carcinogenesis Research Information System

CCRIS

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The repository is no longer available. <<<!!!<<< CCRIS information is migrated to PubChem (https://www.ncbi.nlm.nih.gov/pcsubstance?term=%22Chemical%20Carcinogenesis%20Research%20Information%20System%20(CCRIS)%22%5BSourceName%5D%20AND%20hasnohold%5Bfilt%5D) Help for CCRIS Users in PubChem: https://www.nlm.nih.gov/toxnet/Accessing_CCRIS_Content_from_PubChem.html or PDF: https://www.nlm.nih.gov/toxnet/Accessing_CCRIS_Content_from_PubChem.pdf. >>>!!!>>>

Worldwide Protein Data Bank

wwPDB

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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 coordinates, crystallographic structure factors and NMR experimental data. Aside from coordinates, each deposition also includes the names of molecules, primary and secondary structure information, sequence database references, where appropriate, and ligand and biological assembly information, details about data collection and structure solution, and bibliographic citations. The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. Members are: RCSB PDB (USA), PDBe (Europe) and PDBj (Japan), and BMRB (USA). The wwPDB's mission is to maintain a single PDB archive of macromolecular structural data that is freely and publicly available to the global community.

UCSD Metabolomics Workbench

Metabolomics Workbench

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With the creation of the Metabolomics Data Repository managed by Data Repository and Coordination Center (DRCC), the NIH acknowledges the importance of data sharing for metabolomics. Metabolomics represents the systematic study of low molecular weight molecules found in a biological sample, providing a "snapshot" of the current and actual state of the cell or organism at a specific point in time. Thus, the metabolome represents the functional activity of biological systems. As with other ‘omics’, metabolites are conserved across animals, plants and microbial species, facilitating the extrapolation of research findings in laboratory animals to humans. Common technologies for measuring the metabolome include mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR), which can measure hundreds to thousands of unique chemical entities. Data sharing in metabolomics will include primary raw data and the biological and analytical meta-data necessary to interpret these data. Through cooperation between investigators, metabolomics laboratories and data coordinating centers, these data sets should provide a rich resource for the research community to enhance preclinical, clinical and translational research.

Canadian Biodiversity Information Facility

Système canadien d'information sur la biodiversité

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!!! <<< the repository is offline >>> !!! The CBIF provides primary data on biological species of interest to Canadians. CBIF supports a wide range of social and economic decisions including efforts to conserve our biodiversity in healthy ecosystems, use our biological resources in sustainable ways, and monitor and control pests and diseases. Tools provided by the CBIF include the Integrated Taxonomic Information System (ITIS), Species Access Network, Online Mapping, and the SpeciesBank, including Butterflies of Canada. The CBIF is a member of the Global Biodiversity Information Facility (GBIF).

Yeast Resource Center

Yeast Resource Center Public Data Repository

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The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.

RAM Legacy Stock Assessment Database

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The RAM Legacy Stock Assessment Database is a compilation of stock assessment results for commercially exploited marine populations from around the world. The recently updated database offers many graphical and analytic tools to explore the data, as well as new data sets including; assessments from N.W. Africa, assessments from the Mediterranean Sea, assessments from Chile, data sets on Pacific salmon. The database is seeking collaborators to cover parts of the world that we are missing.

ProteomeXchange

PX

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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. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

PeptideAtlas

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The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.

Cotton EST database

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<<<!!!<<< This repository is no longer available. >>>!!!>>> Database platform for cotton expressed sequence tag (EST)-related information, covering assembled contigs, function annotation, analysis of GO and KEGG, SNP, miRNA, SSR-related marker information.

Code Ocean

CO

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Code Ocean is a cloud-based computational reproducibility platform that provides researchers an easy way to share, discover and run code published in academic journals and conferences.

IRMA Portal

Integrated Resource Management Applications Portal

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IRMA (Integrated Resource Management Applications) provides natural and cultural resources data from the National Park Service. Most entries are in the form of peer-reviewed publications, but some are raw data sets based on in-park research projects.

DataBasin

Data Basin

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Data Basin is a science-based mapping and analysis platform that supports learning, research, and sustainable environmental stewardship.