UniProt: a hub for protein information. UniProt is an important collection of protein sequences and their annotations, which has doubled in size to 80 million sequences during the past year. This growth in sequences has prompted an extension of UniProt accession number space from 6 to 10 characters. An increasing fraction of new sequences are identical to a sequence that already exists in the database with the majority of sequences coming from genome sequencing projects. We have created a new proteome identifier that uniquely identifies a particular assembly of a species and strain or subspecies to help users track the provenance of sequences. We present a new website that has been designed using a user-experience design process. We have introduced an annotation score for all entries in UniProt to represent the relative amount of knowledge known about each protein. These scores will be helpful in identifying which proteins are the best characterized and most informative for comparative analysis. All UniProt data is provided freely and is available on the web at http://www.uniprot.org/.

References in zbMATH (referenced in 136 articles , 1 standard article )

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  1. Consortium, The Uniprot: The universal protein resource (UniProt). (2008) ioport
  2. Foster, J. Nathan; Pilkiewicz, Alexandre; Pierce, Benjamin C.: Quotient lenses (2008)
  3. Lees, Jonathan G.; Janes, Robert W.: Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations (2008) ioport
  4. Mansoori, E. G.; Zolghadri, M. J.; Katebi, S. D.; Mohabatkar, H.; Boostani, R.; Sadreddini, M. H.: Generating fuzzy rules for protein classification (2008)
  5. Mayr, Gabriele; Lepperdinger, Günter; Lackner, Peter: Automated quantitative assessment of proteins’ biological function in protein knowledge bases (2008) ioport
  6. Nikoloski, Zoran; Grimbs, Sergio; May, Patrick; Selbig, Joachim: Metabolic networks are NP-hard to reconstruct (2008)
  7. Pánek, Josef: A comparative computational analysis of protein sequences and literature mining classify `orphan’ neurotransmitter transporters (2008)
  8. Si, Luo; Yu, Danni; Kihara, Daisuke; Fang, Yi: Combining gene sequence similarity and textual information for gene function annotation in the literature (2008) ioport
  9. -: The universal protein resource (UniProt). (2007) ioport
  10. Caffrey, Daniel R.; Dana, Paul H.; Mathur, Vidhya; Ocano, Marco; Hong, Eun-Jong; Wang, Yaoyu E.; Somaroo, Shyamal; Caffrey, Brian E.; Potluri, Shobha; Huang, Enoch S.: PFAAT version 2.0: A tool for editing, annotating, and analyzing multiple sequence alignments (2007) ioport
  11. Carugo, Oliviero: Detailed estimation of bioinformatics prediction reliability through the fragmented prediction performance plots (2007) ioport
  12. Küntzer, Jan; Backes, Christina; Blum, Torsten; Gerasch, Andreas; Kaufmann, Michael; Kohlbacher, Oliver; Lenhof, Hans-Peter: BNDB [8211] the biochemical network database (2007) ioport
  13. Lu, Lingyi; Qian, Ziliang; Cai, Yu-Dong; Li, Yixue: ECS: an automatic enzyme classifier based on functional domain composition (2007)
  14. Mistry, Jaina; Bateman, Alex; Finn, Robert D.: Predicting active site residue annotations in the pfam database (2007) ioport
  15. Porollo, Aleksey; Meller, Jaroslaw: Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D (2007) ioport
  16. Pouliot, Yannick; Karp, Peter D.: A survey of orphan enzyme activities (2007) ioport
  17. Prlić, Andreas; Down, Thomas A.; Kulesha, Eugene; Finn, Robert D.; Kähäri, Andreas; Hubbard, Tim Jp: Integrating sequence and structural biology with DAS (2007) ioport
  18. Schuster-Böckler, Benjamin; Bateman, Alex: Reuse of structural domain-domain interactions in protein networks (2007) ioport
  19. Scott, Michelle S.; Barton, Geoffrey J.: Probabilistic prediction and ranking of human protein-protein interactions (2007) ioport
  20. Shtatland, Timur; Guettler, Daniel; Kossodo, Misha; Pivovarov, Misha; Weissleder, Ralph: Pepbank - a database of peptides based on sequence text mining and public peptide data sources (2007) ioport