ABSTRACT
The AlphaFold Protein Structure Database (AlphaFold DB, https://alphafold.ebi.ac.uk) is an openly accessible, extensive database of high-accuracy protein-structure predictions. Powered by AlphaFold v2.0 of DeepMind, it has enabled an unprecedented expansion of the structural coverage of the known protein-sequence space. AlphaFold DB provides programmatic access to and interactive visualization of predicted atomic coordinates, per-residue and pairwise model-confidence estimates and predicted aligned errors. The initial release of AlphaFold DB contains over 360,000 predicted structures across 21 model-organism proteomes, which will soon be expanded to cover most of the (over 100 million) representative sequences from the UniRef90 data set.
Subject(s)
Databases, Protein , Protein Folding , Proteins/chemistry , Software , Amino Acid Sequence , Animals , Bacteria/genetics , Bacteria/metabolism , Datasets as Topic , Dictyostelium/genetics , Dictyostelium/metabolism , Fungi/genetics , Fungi/metabolism , Humans , Internet , Models, Molecular , Plants/genetics , Plants/metabolism , Protein Conformation, alpha-Helical , Protein Conformation, beta-Strand , Proteins/genetics , Proteins/metabolism , Trypanosoma cruzi/genetics , Trypanosoma cruzi/metabolismABSTRACT
Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among resources, both within the institute and with a wider global infrastructure. Within EMBL-EBI, data resources exchange data through a rich network of data flows mediated by automated systems. This network ensures that users are served with as much information as possible from any search and any starting point within EMBL-EBI's websites. EMBL-EBI data resources also exchange data with hundreds of other data resources worldwide and collectively are a key component of a global infrastructure of interconnected life sciences data resources. We also describe the BioImage Archive, a deposition database for raw images derived from primary research that will supply data for future knowledgebases that will add value through curation of primary image data. We also report a new release of the PRIDE database with an improved technical infrastructure, a new API, a new webpage, and improved data exchange with UniProt and Expression Atlas. Training is a core mission of EMBL-EBI and in 2018 our training team served more users, both in-person and through web-based programmes, than ever before.
Subject(s)
Academies and Institutes , Biological Science Disciplines/organization & administration , Computational Biology/methods , Computational Biology/organization & administration , Databases, Genetic , Data Management , Europe , Humans , Information Storage and RetrievalABSTRACT
The European Bioinformatics Institute (https://www.ebi.ac.uk/) archives, curates and analyses life sciences data produced by researchers throughout the world, and makes these data available for re-use globally (https://www.ebi.ac.uk/). Data volumes continue to grow exponentially: total raw storage capacity now exceeds 160 petabytes, and we manage these increasing data flows while maintaining the quality of our services. This year we have improved the efficiency of our computational infrastructure and doubled the bandwidth of our connection to the worldwide web. We report two new data resources, the Single Cell Expression Atlas (https://www.ebi.ac.uk/gxa/sc/), which is a component of the Expression Atlas; and the PDBe-Knowledgebase (https://www.ebi.ac.uk/pdbe/pdbe-kb), which collates functional annotations and predictions for structure data in the Protein Data Bank. Additionally, Europe PMC (http://europepmc.org/) has added preprint abstracts to its search results, supplementing results from peer-reviewed publications. EMBL-EBI maintains over 150 analytical bioinformatics tools that complement our data resources. We make these tools available for users through a web interface as well as programmatically using application programming interfaces, whilst ensuring the latest versions are available for our users. Our training team, with support from all of our staff, continued to provide on-site, off-site and web-based training opportunities for thousands of researchers worldwide this year.
