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Benchmark Energy & Geometry Database (BEGDB)
09 May 2024
The Benchmark Energy & Geometry Database (BEGDB) collects results of highly accurate QM calculations of molecular structures, energies and properties. These data can serve as benchmarks for testing and parameterization of other computational methods.
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BIGNASim
09 May 2024
BIGNASim, a comprehensive platform including a database system and an analysis portal, aimed to be a general database for handling nucleic acids simulations.
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BioFragment Database (BFDb)
09 May 2024
The BioFragment Database (BFDb) is an open-data platform for computational chemistry analysis of noncovalent interactions and collects >3000 bifragment contacts directly from biological systems.
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BRENDA
09 May 2024
BRENDA is the main collection of enzyme functional data available to the scientific community.
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CAZY
09 May 2024
The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.
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DipCheck
09 May 2024
DipCheck is a validation tool for the evaluation of protein backbone geometry, developed by Joana Pereira and Victor Lamzin at the EMBL Hamburg. The tool uses a Euclidian 3D space (DipSpace) of the orthogonal descriptors of the geometry of a 5-atom dipeptide unit:...
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European Variation Archive (EVA)
09 May 2024
The European Variation Archive (EVA) is an open-access database of all types of genetic variation data from all species.
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IntAct Molecular Interaction Database
09 May 2024
IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
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IntEnz
09 May 2024
IntEnz (Integrated relational Enzyme database) is a freely available resource focused on enzyme nomenclature. IntEnz is created in collaboration with the Swiss Institute of Bioinformatics (SIB). This collaboration is responsible for the production of the ENZYME...
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InterRidge Vents Database
09 May 2024
InterRidge Vents Database is to provide a comprehensive list of active submarine hydrothermal vent fields for use in academic research and education.
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maizeGDB
09 May 2024
MaizeGDB (maize genetics and genomics database) is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.
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MetaboLights
09 May 2024
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and...
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MetalPDB
09 May 2024
MetalPDB collects and allows easy access to the knowledge on metal sites in biological macromolecules, starting from the structural information contained in the Protein Data Bank (PDB).
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MicroScope
09 May 2024 | Science Gateways
MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation.
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Molecular Space
09 May 2024 | Science Gateways
The Clean Energy Project (CEP) is a virtual high-throughput discovery and design effort for the next generation of plastic solar cell materials. We study millions of candidate structures to identify suitable compounds for the harvesting of renewable energy from the...
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Neotoma Paleoecology Database
09 May 2024 | Science Gateways
Neotoma Paleoecology Database and Community is an online hub for data, research, education, and discussion about paleoenvironments. Anyone with an Internet connection can access Neotoma.
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ODM2(Observations Data Model 2)
09 May 2024 | Science Gateways
ODM2 is an information model and supporting software ecosystem for feature-based earth observations, designed to facilitate interoperability across scientific disciplines and domain cyberinfrastructures. For example, a single ODM2 database can readily integrate...
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OMA
09 May 2024 | Science Gateways
The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes.
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Paleobiology Database (PBDB)
09 May 2024 | Science Gateways
The Paleobiology Database is a public database of paleontological data that anyone can use, maintained by an international non-governmental group of paleontologists. You can explore the data online in the Navigator, which lets you filter fossil occurrences by time,...
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PHARMACOLOGY
09 May 2024 | Science Gateways
One of the main aims is to provide a searchable database with quantitative information on drug targets and the prescription medicines and experimental drugs that act on them. The information in the database is presented at two levels: the initial view or landing...
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Phylogeny.fr
09 May 2024 | Science Gateways
Phylogeny.fr has been designed to provide a high performance platform that transparently chains programs relevant to phylogenetic analysis in a comprehensive, and flexible pipeline. Although phylogenetic aficionados will be able to find most of their favorite tools...
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PLEXdb
09 May 2024 | Science Gateways
PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to related genetic,...
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Reactome
09 May 2024 | Science Gateways
REACTOME is an open-source, open access, manually curated and peer-reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic and clinical research, genome...
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Rhea
09 May 2024 | Science Gateways
Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models.
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SwissRegulon Portal
09 May 2024 | Science Gateways
A repository of computational biology tools and databases developed by the van Nimwegen lab