D2P2: database of disordered protein predictions
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No Canadian affiliation. An affiliation-only frame — the usual design — would never have seen this work. It is one of the works that make the case for inverting the frame.
Abstract
We present the Database of Disordered Protein Prediction (D(2)P(2)), available at http://d2p2.pro (including website source code). A battery of disorder predictors and their variants, VL-XT, VSL2b, PrDOS, PV2, Espritz and IUPred, were run on all protein sequences from 1765 complete proteomes (to be updated as more genomes are completed). Integrated with these results are all of the predicted (mostly structured) SCOP domains using the SUPERFAMILY predictor. These disorder/structure annotations together enable comparison of the disorder predictors with each other and examination of the overlap between disordered predictions and SCOP domains on a large scale. D(2)P(2) will increase our understanding of the interplay between disorder and structure, the genomic distribution of disorder, and its evolutionary history. The parsed data are made available in a unified format for download as flat files or SQL tables either by genome, by predictor, or for the complete set. An interactive website provides a graphical view of each protein annotated with the SCOP domains and disordered regions from all predictors overlaid (or shown as a consensus). There are statistics and tools for browsing and comparing genomes and their disorder within the context of their position on the tree of life.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
The record
- Venue
- Nucleic Acids Research
- Topic
- Protein Structure and Dynamics
- Field
- Biochemistry, Genetics and Molecular Biology
- Canadian institutions
- —
- Funders
- Russian Academy of SciencesBiotechnology and Biological Sciences Research CouncilNatural Sciences and Engineering Research Council of CanadaEngineering and Physical Sciences Research CouncilDirectorate for Biological SciencesUniversity of AlbertaNational Science Foundation
- Keywords
- BiologyContext (archaeology)GenomeProteomeDownloadParsingSet (abstract data type)Source codeComputational biologyTree (set theory)Computer scienceBioinformaticsGeneticsArtificial intelligenceWorld Wide WebGeneProgramming language
- Has abstract in OpenAlex
- yes