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http://www.ebi.ac.uk/pdbsum

Pictorial database of an at-a-glance overview of the contents of each 3D structure deposited in the Protein Data Bank (PDB). It shows the molecule(s) that make up the structure (ie protein chains, DNA, ligands and metal ions) and schematic diagrams of their interactions. Extensive use is made of the freely available RasMol molecular graphics program to view the molecules and their interactions in 3D. Entries are accessed either by their 4-character PDB code, or by one of the two search boxes provided on the PDBsum home page: text search or sequence search. The information given on each PDBsum entry is spread across several pages, as listed below and accessible from the tabs at the top of the page. Only the relevant tabs will be present on any given page. * Top page - summary information including thumbnail image of structure, molecules in structure, enzyme reaction diagram (where relevant), GO functional assignments, and selected figures from key reference * Protein - wiring diagram, topology diagram(s) by CATH domain, and residue conservation (where available) * DNA/RNA - DNA/RNA sequence and NUCPLOT showing interactions made with protein * Ligands - description of bound molecule and LIGPLOT showing interactions made with protein * Prot-prot - schematic diagrams of any protein-protein interfaces and the residue-residue interactions made across them * Clefts - listing of top ten clefts in the surface of the protein, listed by volume with any bound ligands shown * Links - links to external databases Additionally, it accepts users'''' own PDB format files and generates a private set of analyses for each uploaded structure.

Proper citation: PDBsum (RRID:SCR_006511) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/enzymes/

Database of known enzyme structures that have been deposited in the Protein Data Bank (PDB). The enzyme structures are classified by their E.C. number of the ENZYME Data Bank. Browse the classification hierarchy or enter an EC number or search-string. There are currently 45,638 PDB-enzyme entries in the PDB (as at 23 February, 2013) involving 38,109 separate PDB files - some files having more than one E.C. number associated with them.

Proper citation: Enzyme Structures Database (RRID:SCR_007125) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/sas/

SAS is a tool for applying structural information to a given protein sequence. It uses FASTA to scan a given protein sequence against all the proteins of known 3D structure in the Protein Data Bank (PDB). The resultant multiple alignment can be colored according to different structural features and the matching 3D structures can be superimposed and viewed in RasMol. Use the form to identify your protein sequence of interest by: a) providing a PDB code, b) providing a UniProt code or accession number, c) pasting in your sequence, or d) uploading a PDB file. By default the whole PDB will be searched, but you can restrict the search using the Search Option box at the bottom.

Proper citation: SAS - Sequence Annotated by Structure (RRID:SCR_004635) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/

Non-profit academic organization for research and services in bioinformatics. Provides freely available data from life science experiments, performs basic research in computational biology, and offers user training programme, manages databases of biological data including nucleic acid, protein sequences, and macromolecular structures. Part of EMBL.

Proper citation: European Bioinformatics Institute (RRID:SCR_004727) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/archschema/

ArchSchema is a java webstart application that generates dynamic plots of related Pfam domain architectures. The protein sequences having each architecture can be displayed on the plot and separately listed. Where there is 3D structural information in the PDB, the relevant PDB codes can be shown on the plot. Sequences can be be filtered by organism, or the output can be limited to just those protein sequences for which there is structural information in the PDB. Search by UniProt sequence id, or by Pfam domain id. Red underlines indicate the extent to which 3D structures of the domains and architectures are available in the PDB. Left-clicking on a node shows a panel containing information about the constituent domains, the protein sequences having the given architecture, and any sequences that have whole or partial structures in the PDB. You can display protein sequence (or, alternatively, the protein structures) associated with each architecture. You can download ArchSchema to run locally from your own machine. Note, however, you only download the code and not the data. Thus you will need to be connected to the Internet whenever you perform a search from within ArchSchema. The search initiates a call to the EBI which returns the data to ArchSchema for graphing.

Proper citation: ArchSchema (RRID:SCR_004947) Copy   

•   Source: SciCrunch Registry

http://www.rcsb.org/#Category-welcome

Collection of structural data of biological macromolecules. Database of information about 3D structures of large biological molecules, including proteins and nucleic acids. Users can perform queries on data and analyze and visualize results.

Proper citation: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) (RRID:SCR_012820) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/profunc/index.html

The ProFunc server had been developed to help identify the likely biochemical function of a protein from its three-dimensional structure. It uses both sequence- and structure-based methods including fold matching, residue conservation, surface cleft analysis, and functional 3D templates, to identify both the protein''''s likely active site and possible homologues in the PDB. Often, where one method fails to provide any functional insight another may be more helpful. You can submit your own structure, analyze an existing PDB entry, or retrieve the results of a previously submitted run. The files are usually stored for about 6 months before being deleted. However, they are stored on a partition that is not backed up; so, in principle, they could disappear at any time.

Proper citation: ProFunc (RRID:SCR_004450) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/drugport/

DrugPort provides an analysis of the structural information available in the Protein Data Bank (PDB) relating to drug molecules and their protein targets. The drug-target data comes from the DrugBank database. You can search the entries by identifier, test or by protein sequence, or you can use the browse options in the menu on the left.

Proper citation: DrugPort (RRID:SCR_006573) Copy   

•   Source: SciCrunch Registry