-
BamBam
09 May 2024
BamBam is a package of tools for genome sequence analysis. BamBam contains tools that facilitate summarizing data from BAM alignment files and identifying features such as SNPs, indels, and haplotypes represented in those alignments. It aims to use parameters that...
-
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.
-
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.
-
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.
-
BRENDA
09 May 2024
BRENDA is the main collection of enzyme functional data available to the scientific community.
-
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.
-
CottonGen
09 May 2024
CottonGen is a new cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure.
-
Crops in silico
09 May 2024
Crops in silico is a global scientific collaboration that aims to harness the great strides in understanding of plant function from genes to whole plants, to accelerate forward approaches to crop breeding and bioengineering. The Crops in silico community is comprised...
-
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:...
-
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.
-
Genome Database for Rosaceae (GDR)
09 May 2024
The Genome Database for Rosaceae is a curated and integrated web-based relational database providing data mining tools and publicly available genomics, genetics and breeding data for Rosaceae (almond, apple, blackberry, cherry, peach, pear, plum, raspberry, rose, and...
-
Genomics Virtual Laboratory (GVL)
09 May 2024
The Genomics Virtual Laboratory (GVL) provides a cloud-based suite of genomics analysis tools for research and training.
-
Genomicus
09 May 2024
Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. Once a query gene has been entered, it is displayed in...
-
GenSAS
09 May 2024
The Genome Sequence Annotation Server (GenSAS) is an online platform that provides a pipeline for whole genome structural and functional annotation. Users can upload genome sequences and select from a variety of tools for repeat masking, prediction of gene models and...
-
HRGRN
09 May 2024
We developed HRGRN, a Graph search-empowered integrative database of Arabidopsis signaling transduction, metabolism, and gene regulation networks, with an emphasis on hormone signaling and gene regulatory pathways. The database is designed to host and discover...
-
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.
-
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...
-
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.
-
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.
-
Medicago truncatula genome database
09 May 2024
Medicago truncatula, a close relative of alfalfa, is a preeminent model for the study of the processes of nitrogen fixation, symbiosis, and legume genomics. The sequencing project was initiated with a generous grant from Samuel Roberts Noble Foundation (link is...
-
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...
-
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).
-
MicroScope
09 May 2024 | Science Gateways
MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation.
-
MicroScope
09 May 2024 | Science Gateways
MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation.
-
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...