European UniProt

The characterization as a target protein might become possible through the combination of textual information with entries from databases such as UniProt,14 PubChem,15 or DrugBank.16 At ChEBI,17 the European Bioinformatics Institute s database on bioactive small molecules, this integration of chemical information with biological entities is realized through expert curation of entries and introduction to referential links to databases such as UniProt and PDB. 

Universal Protein Knowledgebase (UniProt). European Bioinformatics Institute (EBI), Swiss Institute of Bioinformatics (SIB), Protein Information Resource (PIR), Georgetown Univ. URL http //www.uniprot.org. Central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. A central access point for extensive curated protein information, including function, classification, and cross-reference. 

The SRS 3D Viewer [28] is part of the SRS 3D server at the European Bioinformatics Institute (EBI) site (http //srs3d.ebi.ac.uk). Similar to Cn3D, SRS 3D is intuitive and easy to use. It enables the user to easily find all related structures, select one, and immediately see where the target sequence aligns onto the 3D structure (fig. 11.2B). Key differences between Cn3D and SRS 3D are that SRS 3D shows sequence features from the UniProt, InterPro, and PDB entries of the target sequence and enables users to easy map these features onto the structures (fig. 11.2C). SRS 3D also has a richer set of mouse and keyboard commands to help navigate and select parts of the sequence and structure. However, a drawback of the SRS 3D Viewer is that it can be difficult to install on some computers. SRS 3D is a commercial product but can be used freely via the Web to view any 3D structures in the PDB. 

Field/value-based flat files have been very commonly used in bioinformatics. Examples are the flat file libraries from GenBank, European Molecular Biology Laboratory Nucleotide Sequence Database (EMBL), DNA Data Bank of Japan, or Universal Protein Resource (UniProt). These file types are a very limited solution because they lack referencing, vocabulary control, and constraints. In addition, on the file level, there is no inherent locking mechanism that detects when a file is being used or modified. However, these file types are primarily used for reading purposes. 

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