BioData Services

SILVA

SILVA is the European ribosomal RNA gene database. It provides comprehensive, quality checked and regularly updated datasets of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya). Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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SILVAngs

SILVAngs is a data analysis service for ribosomal RNA gene (rDNA) amplicon reads from high-throughput sequencing (next-generation sequencing (NGS)) approaches based on an automatic software pipeline. It uses the SILVA rDNA databases, taxonomies, and alignments as a reference. It facilitates the classification of rDNA reads and provides a wealth of results (tables, graphs and sequence files) for download. Find this service in BioTools here.
Funding: Not de.NBI funded.

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PANGAEA

PANGAEA as Data Publisher for Earth & Environmental Science is a globally leading information system, long term archive and data publisher for geoscientific, biological and environmental data. Data published by PANGAEA origins from a broad range of subdisciplines of the Biological Sciences, Chemistry, Physics with a special focus an Earth Sciences and Environmental Sciences. Essential services supplied by PANGAEA are data curation, long-term data archiving and data publication. Data curation includes quality control of metadata and the development of ontologies as well as vocabularies according to international protocols and standards. Metadata are extensive and each dataset can be cited using a universally unique Digital Object Identifier (DOI).
Funding: Development and maintenance partially funded by de.NBI.

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BRENDA

BRENDA is the world's largest and most widely used information system on all aspects of enzymes, including function, structure, mutants, properties like stability, purification, involvement in diseases etc. The – all together 150 million data in the database are compiled via manual extraction from the primary literature (4 million from >132 000 papers), data integration from e.g. sequence and structure databases, and calculation (genome annotation, membrane association, statistics). Textual and structural input of queries is posssible as well as browsing in EC-. Taxonomy-, ontology-trees. Data download is possible via SOAP. Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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BacDive

BacDive - The Bacterial Diversity Metadatabase focuses providing organism-linked information covering the multifarious aspects of bacterial biodiversity. The BacDive portal offers information on taxonomic classification, morphology, physiology, cultivation, origin and natural habitat for more than 50,000 bacterial and archeal strains. Where available, links are given to access the respective biological resources and the associated sequence data via the INSDC accession numbers for genomes and 16S rRNA. In addition to the advanced search functionallities of the web portal access, BacDive offers data retrieval via a web service api or individual compilations of data sets that can be exported to CSV spreadsheet files. Find this service in BioTools here.
Funding: Development and maintenance partially funded by de.NBI.

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ProteinsPlus

ProteinsPlus ia a web portal for protein structure-based life science research. It provides essential structure analysis, preprocessing, and prediction tools which support the retrieval and interpretation of publicly available protein structures.It comprises the following services:

  • DoGSiteScorer is an automated pocket detection and analysis tool enabling the identification of potential protein binding pockets and subpockets, the calculation of their shape and physicochemical properties and the estimation of their druggability.

  • EDIA is an easily interpretable electron density score for individual atoms which quantifies the electron density support of each single atom. Atomic EDIA values can further be combined to compute an electron density score for small molecules, fragments, or residues.

  • Starting with 3D protein-ligand structures, PoseView automatically creates two-dimensional diagrams which depict the protein-ligand interactions and conform to chemical drawing conventions.

  • PPI classifies a protein-protein complex concerning its interaction type into permanent, transient or crystal artifact.

  • Protoss adds missing hydrogen atoms to protein structures and optimizes the hydrogen bonding network under consideration of alternative protonation states, tautomers, and hydrogen coordinates of both, protein and ligand molecules.

  • SIENA facilitates a search for homologous protein binding sites structures in the Protein Data Bank. It allows an automated case-specific assembly and preprocessing of protein structure ensembles supporting protein flexibility and point mutation analyses as well as structure-based virtual screening.

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