title: TOPDOM: database of conservatively located domains and motifs in proteins.
abstract: The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins.
  
  
  
  TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer.
  
  
  
  tusnady.gabor@ttk.mta.hu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest H-1518, Hungary.
authors.forename: Julia
authors.initials: J
authors.lastname: Varga
authors.affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest H-1518, Hungary.
authors.forename: László
authors.initials: L
authors.lastname: Dobson
authors.affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest H-1518, Hungary.
authors.forename: Gábor E
authors.initials: GE
authors.lastname: Tusnády
mesh_terms: D000465:Algorithms; D020816:Amino Acid Motifs; D017124:Conserved Sequence; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval; D008565:Membrane Proteins; D000072417:Protein Domains; D017434:Protein Structure, Tertiary; D011506:Proteins; D016415:Sequence Alignment; D012984:Software; D014584:User-Computer Interface
chemical_list: D008565:Membrane Proteins; D011506:Proteins