TOPDB database User's Manual
Documents related to TOPDB
Documents related to the database structure and the contents can be found under the Documents menu. Short and detailed description (manual), manuscript of the publication of TOPDB, and several supplementary information for database content and organization.
Short description of TOPDB
Short description of the establishment, the structure, the organization, and the aims of the database. A good resource for a brief summary for TOPDB.
The manuscript(s) of the publication(s) related to the TOPDB in downloadable format. If you find TOPDB useful in your research, please cite our articles.
Help pages and documentation for the TOPDB database.
In the TOPDB database, we strictly determine the outside and inside for membrane types. As a basis, cytoplasmic face of the membrane is always inside, all the other spaces, and membrane faces are nominated relative to the cytoplasm. We always use the RED color for the inside space, and the BLUE color for the outside place. The flash movie under the Membranes menu gives an overview about the membrane types used in the TOPDB (and SwissProt) database. The colored graphical implementation of the membranes, and compartments containing multiple types of membranes help to understand the position and orientation of the apropriate protein.
List of experiment types used to determine topologies
Data in the TOPDB database is extracted from experiments related to the topology of proteins. A complete and up-to-date list of the experiment types with a brief description and subtypes can be found under the Experiments menu.
Description of CCTOP algorithm
Description of CCTOP algorithm.
Calculation of reliability
Calculation of reliability of the final CCTOP prediction.
TOPDB Schema definition
The TOPDB database uses XML data structure to store the topology data. The TOPDB schema file (TOPDB.xsd) is accessible under TOPDB Schema menu. XML Schemas express shared vocabularies and allow machines to interpret rules made by people. They provide means for defining the structure, content and semantics of XML documents in more detail. XML Schema was approved as a W3C Recommendation on 2 May 2001 and a second edition incorporating many errata was published on 28 October 2004.
Disclaimer, Copyright and Privacy information about the TOPDB database.
The most up-to-date version of the database is accessible under the download menu in XML and traditional formats (whole database, topologies only, and sequences only). Besides the most current, all previous database releases are also accessible through the subversion based version control system.
Quick searches can be performed from the field provided in the header of the homepage. Advanced search also available under the search menu, where several additional filter can be applied to the query.
If the search results in several entries, the server send back a brief, selectable list of the matched entries, while in the case of a single hit the data of the entry found is visualized instantly.
List of the search results
If multiple hits are found, a protein can be selected from a list, where the protein and organism names are indicated next to the TOPDB identification number.
Database record of an entry
For each entry, numerous possibilities are provided to help to understand data. The various visualization modes can be selected by clicking the appropriate tab on the result page. The flash movie shows the topology model of proteins, with clickable sequence parts. By selecting a given region, experiments related to that region are shown in a new pop-up window. On graphical view, experiments are grouped by references, and are mapped to the protein sequence, which is represented by a horizontal line. Moving the mouse over a coloured box on the image, a small window containing the experimental details and links to related references is opening. In html view data are shown in tabular form, while choosing xml tab, the raw xml file is shown. Two more tabs are given on show page, the history and download tabs. On history tab the history of the given entry can be traced back, while clicking the download tab, the given entry can be downloaded separately (in xml format).
A brief summary of statistics is always visible on the the bottom-left side of the homepage. Detailed statistics about experiment types, protein types, etc. are calculated dynamically and given under the Statistics menu.
Contact information about the most competent person can be found under the Contact menu.
Word Wide Web Servers, Services and Databases related to transmembrane proteins.