mpstruc is part of the Structural Biology Knowledgebase SBKB
When referencing this page, please use this url: http://blanco.biomol.uci.edu/mpstruc/
 

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  • MPtopo XML data representations now available: XML representations are now available for the MPtopo membrane protein topology database.
  • MPtopo integrated into mpstruc: MPtopo, our curated database of membrane proteins with experimentally validated transmembrane segments, has a new structure and interface: It is now integrated with mpstruc (e.g., see the mpstruc entry for 2BRD for a link to mptopo). MPEx has also been updated to use the new mptopo.
  • Mpstruc XML interface updated: We have introduced URLs that provide direct access to XML representations of mpstruc data without having to visit the mpstruc web page. These URLs allow users' software tools to access the data directly. See the new expandable XML Representations section of the mpstruc page.

Latest new protein entered: 18 Oct 2014 at 17:06 PDT.
Last database update: 18 Oct 2014 at 17:07 PDT

New Structures:
Unique proteins in database = 504
Coördinate files in database = 1545
Published reports of membrane protein structures in database = 906
(Counts do not include pre-publication structures)

Unique proteins include proteins of same type from different species. For example, photosynthetic reaction centers from R. viridis and R. sphaeroides are considered unique. Structures of mutagenized versions of proteins already in the database are excluded as unique. Proteins that differ only by substrate bound or by physiological state are also excluded. Structures 'obsoleted' by the PDB are not included.

Total number of PDB coördinate files, including those for unique proteins. This number reflects the fact that published reports of structures often include several coördinate files describing, for example, the protein in different crystal forms, or with different bound substrates.


Pre-Publication Structures (link to mpstruc bulletin board page)
 
A word about the new interface to the protein table.
XML Representations

An XML representation provides a convenient machine or human readable format of the portion of the data table that has been made visible, and allows you to build software tools to consume it as you see fit. You can use the URLs adjacent to the buttons below to access the same view the corresponding button provides.

This button generates an XML representation of the currently visible portion of the table.

http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucTblXml
http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucMonotopicTblXml
http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucBetaBrlTblXml
http://blanco.biomol.uci.edu/mpstruc/listAll/mpstrucAlphaHlxTblXml

If your browser doesn’t directly display a nicely formatted XML page, it should provide a "view page source" menu selection that will. It should also provide a "save page" option so that you can download the XML formatted data.

If you’re not familiar with XML and how to use it, a good source of information is available here.

NOTES:

Generated XML includes the following Document Type Definition (DTD):

<!DOCTYPE mpstruc [
  <!ELEMENT mpstruc (caption,groups*)>
  <!ATTLIST mpstruc createdBy CDATA #REQUIRED>
  <!ATTLIST mpstruc maintainedBy CDATA #REQUIRED>
  <!ATTLIST mpstruc copyright CDATA #REQUIRED>
  <!ATTLIST mpstruc url CDATA #REQUIRED>
  <!ATTLIST mpstruc lastNewProteinDate CDATA #REQUIRED>
  <!ATTLIST mpstruc lastDatabaseEditDate CDATA #REQUIRED>
  <!ATTLIST mpstruc timeStamp CDATA #REQUIRED>
  <!ELEMENT caption (#PCDATA)>
  <!ELEMENT groups (group*)>
  <!ELEMENT group (name,proteins,subgroups)>
  <!ELEMENT subgroups (subgroup*)>
  <!ELEMENT subgroup (name,proteins)>
  <!ELEMENT name (#PCDATA)>
  <!ELEMENT proteins (protein*)>
  <!ELEMENT memberProteins (memberProtein*)>
  <!ELEMENT protein (pdbCode,name,species,taxonomicDomain,expressedInSpecies,resolution,description,bibliography,
                     secondaryBibliographies,relatedPdbEntries,memberProteins)>
  <!ELEMENT memberProtein (pdbCode,masterProteinPdbCode,name,species,expressedInSpecies,resolution,
                           description,bibliography,secondaryBibliographies,relatedPdbEntries)>
  <!ELEMENT pdbCode (#PCDATA)>
  <!ELEMENT masterProteinPdbCode (#PCDATA)>
  <!ELEMENT species (#PCDATA)>
  <!ELEMENT taxonomicDomain (#PCDATA)>
  <!ELEMENT expressedInSpecies (#PCDATA)>
  <!ELEMENT resolution (#PCDATA)>
  <!ELEMENT description (#PCDATA)>
  <!ELEMENT bibliography (pubMedId,authors,year,title,journal,volume,issue,pages,doi,notes)>
  <!ELEMENT pubMedId (#PCDATA)>
  <!ELEMENT authors (#PCDATA)>
  <!ELEMENT year (#PCDATA)>
  <!ELEMENT title (#PCDATA)>
  <!ELEMENT journal (#PCDATA)>
  <!ELEMENT volume (#PCDATA)>
  <!ELEMENT issue (#PCDATA)>
  <!ELEMENT pages (#PCDATA)>
  <!ELEMENT doi (#PCDATA)>
  <!ELEMENT notes (#PCDATA)>
  <!ELEMENT secondaryBibliographies (bibliography*)>
  <!ELEMENT relatedPdbEntries (pdbCode*)>
]>

 
Links to the Protein Data Bank Site
Links to the Structural Biology Knowledgebase Site
Membrane Proteins of Known 3D Structure
(Table description)
Protein
PDB Code Links Reference
(links are to PubMed)
MONOTOPIC MEMBRANE PROTEINS
TRANSMEMBRANE PROTEINS: BETA-BARREL
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL