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TOPDB: topology data bank of transmembrane proteins.

Tusnády GE, Kalmár L, Simon I - Nucleic Acids Res. (2007)

Bottom Line: It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins.The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization.TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins.

View Article: PubMed Central - PubMed

Affiliation: Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary.

ABSTRACT
The Topology Data Bank of Transmembrane Proteins (TOPDB) is the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information currently available. It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins. In addition to experimental data from the literature, an extensive collection of structural data was also compiled from PDB and from PDBTM. Because topology information is often incomplete, for each protein in the database the most probable topology that is consistent with the collected experimental constraints was also calculated using the HMMTOP transmembrane topology prediction algorithm. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization. TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins. TOPDB is available at http://topdb.enzim.hu.

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Related in: MedlinePlus

The graph shows the topology of TOPDB entry of mouse multidrug resistance protein 1 (AP00199). The distinct experiments have unique identifiers (e.g. PDB ID, PUBMED ID, etc.), and if the topology data are derived from homologous proteins the identifier is extended with the TOPDB ID. The graph is colour coded to show protein segment localization: membrane interior (red), membrane exterior (blue) and transmembrane (yellow). In the interactive view, additional information can be obtained by rolling the mouse over the individual bars, e.g. experiment type, residue position and cross references.
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Figure 2: The graph shows the topology of TOPDB entry of mouse multidrug resistance protein 1 (AP00199). The distinct experiments have unique identifiers (e.g. PDB ID, PUBMED ID, etc.), and if the topology data are derived from homologous proteins the identifier is extended with the TOPDB ID. The graph is colour coded to show protein segment localization: membrane interior (red), membrane exterior (blue) and transmembrane (yellow). In the interactive view, additional information can be obtained by rolling the mouse over the individual bars, e.g. experiment type, residue position and cross references.

Mentions: Although XML format is useful for computer programming, it is hard to understand the raw data. Therefore, numerous possibilities are provided to help the interpretation of data. Various visualization modes can be selected by clicking the appropriate tab on the Result page. Users can choose between graphical representations (flash movie or image) or text representations (HTML or XML). The flash movie shows the topology model of proteins with clickable sequence parts. By selecting a given region, the experiments related to the specified region appear in a new pop-up window. In the graphical view, experiments are grouped by references, and are mapped on the protein sequence, which is represented by a horizontal line. A colour code helps to grasp the image at a glance (Figure 2). Moving the mouse over a coloured box on the image opens a small window containing the experimental details and links to related references. In HTML view, data are shown in a tabular form, while choosing XML tab, the raw XML file is shown. On an additional tab, the history of the given entry can be traced back, while by clicking the download tab, the selected entry can be downloaded separately (in XML format).Figure 2.


TOPDB: topology data bank of transmembrane proteins.

Tusnády GE, Kalmár L, Simon I - Nucleic Acids Res. (2007)

The graph shows the topology of TOPDB entry of mouse multidrug resistance protein 1 (AP00199). The distinct experiments have unique identifiers (e.g. PDB ID, PUBMED ID, etc.), and if the topology data are derived from homologous proteins the identifier is extended with the TOPDB ID. The graph is colour coded to show protein segment localization: membrane interior (red), membrane exterior (blue) and transmembrane (yellow). In the interactive view, additional information can be obtained by rolling the mouse over the individual bars, e.g. experiment type, residue position and cross references.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238857&req=5

Figure 2: The graph shows the topology of TOPDB entry of mouse multidrug resistance protein 1 (AP00199). The distinct experiments have unique identifiers (e.g. PDB ID, PUBMED ID, etc.), and if the topology data are derived from homologous proteins the identifier is extended with the TOPDB ID. The graph is colour coded to show protein segment localization: membrane interior (red), membrane exterior (blue) and transmembrane (yellow). In the interactive view, additional information can be obtained by rolling the mouse over the individual bars, e.g. experiment type, residue position and cross references.
Mentions: Although XML format is useful for computer programming, it is hard to understand the raw data. Therefore, numerous possibilities are provided to help the interpretation of data. Various visualization modes can be selected by clicking the appropriate tab on the Result page. Users can choose between graphical representations (flash movie or image) or text representations (HTML or XML). The flash movie shows the topology model of proteins with clickable sequence parts. By selecting a given region, the experiments related to the specified region appear in a new pop-up window. In the graphical view, experiments are grouped by references, and are mapped on the protein sequence, which is represented by a horizontal line. A colour code helps to grasp the image at a glance (Figure 2). Moving the mouse over a coloured box on the image opens a small window containing the experimental details and links to related references. In HTML view, data are shown in a tabular form, while choosing XML tab, the raw XML file is shown. On an additional tab, the history of the given entry can be traced back, while by clicking the download tab, the selected entry can be downloaded separately (in XML format).Figure 2.

Bottom Line: It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins.The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization.TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins.

View Article: PubMed Central - PubMed

Affiliation: Institute of Enzymology, BRC, Hungarian Academy of Sciences, Budapest, Hungary.

ABSTRACT
The Topology Data Bank of Transmembrane Proteins (TOPDB) is the most complete and comprehensive collection of transmembrane protein datasets containing experimentally derived topology information currently available. It contains information gathered from the literature and from public databases available on the internet for more than a thousand transmembrane proteins. TOPDB collects details of various experiments that were carried out to learn about the topology of particular transmembrane proteins. In addition to experimental data from the literature, an extensive collection of structural data was also compiled from PDB and from PDBTM. Because topology information is often incomplete, for each protein in the database the most probable topology that is consistent with the collected experimental constraints was also calculated using the HMMTOP transmembrane topology prediction algorithm. Each record in TOPDB also contains information on the given protein sequence, name, organism and cross references to various other databases. The web interface of TOPDB includes tools for searching, relational querying and data browsing as well as for visualization. TOPDB is designed to bridge the gap between the number of transmembrane proteins available in sequence databases and the publicly accessible topology information of experimentally or computationally studied transmembrane proteins. TOPDB is available at http://topdb.enzim.hu.

Show MeSH
Related in: MedlinePlus