Review

Cellular and Molecular Life Sciences

, Volume 67, Issue 7, pp 1049-1064

First online:

Open Access This content is freely available online to anyone, anywhere at any time.

From protein sequences to 3D-structures and beyond: the example of the UniProt Knowledgebase

  • Ursula HinzAffiliated withSwiss-Prot Group, Swiss Institute of Bioinformatics Email author 
  • , The UniProt ConsortiumAffiliated withSwiss-Prot Group, Swiss Institute of BioinformaticsVital-IT Group, Swiss Institute of BioinformaticsDepartment of Structural Biology and Bioinformatics, Faculty of Medicine, University of GenevaThe European Bioinformatics Institute (EBI), The EMBL OutstationProtein Information Resource, Georgetown University

Abstract

With the dramatic increase in the volume of experimental results in every domain of life sciences, assembling pertinent data and combining information from different fields has become a challenge. Information is dispersed over numerous specialized databases and is presented in many different formats. Rapid access to experiment-based information about well-characterized proteins helps predict the function of uncharacterized proteins identified by large-scale sequencing. In this context, universal knowledgebases play essential roles in providing access to data from complementary types of experiments and serving as hubs with cross-references to many specialized databases. This review outlines how the value of experimental data is optimized by combining high-quality protein sequences with complementary experimental results, including information derived from protein 3D-structures, using as an example the UniProt knowledgebase (UniProtKB) and the tools and links provided on its website (http://​www.​uniprot.​org/​). It also evokes precautions that are necessary for successful predictions and extrapolations.

Keywords

Data flood Annotation Swiss-Prot Knowledgebase UniProtKB Proteomics Structural genomics Protein 3D-structure