title: TSTMP: target selection for structural genomics of human transmembrane proteins.
abstract: The TSTMP database is designed to help the target selection of human transmembrane proteins for structural genomics projects and structure modeling studies. Currently, there are only 60 known 3D structures among the polytopic human transmembrane proteins and about a further 600 could be modeled using existing structures. Although there are a great number of human transmembrane protein structures left to be determined, surprisingly only a small fraction of these proteins have 'selected' (or above) status according to the current version the TargetDB/TargetTrack database. This figure is even worse regarding those transmembrane proteins that would contribute the most to the structural coverage of the human transmembrane proteome. The database was built by sorting out proteins from the human transmembrane proteome with known structure and searching for suitable model structures for the remaining proteins by combining the results of a state-of-the-art transmembrane specific fold recognition algorithm and a sequence similarity search algorithm. Proteins were searched for homologues among the human transmembrane proteins in order to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome. The pipeline constructed for creating the TSTMP database guarantees to keep the database up-to-date. The database is available at http://tstmp.enzim.ttk.mta.hu.
authors.affiliation: Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rakpart 3, H1111 Hungary.
authors.forename: Julia
authors.initials: J
authors.lastname: Varga
authors.affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, 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 PO Box 7, H-1518 Hungary.
authors.forename: István
authors.initials: I
authors.lastname: Reményi
authors.affiliation: 'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518 Hungary tusnady.gabor@ttk.mta.hu.
authors.forename: Gábor E
authors.initials: GE
authors.lastname: Tusnády
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D023281:Genomics / Q000379:methods*; D006801:Humans; D008565:Membrane Proteins / Q000737:chemistry / Q000235:genetics; D008958:Models, Molecular; D011487:Protein Conformation; D020543:Proteome; D040901:Proteomics / Q000379:methods; D013329:Structure-Activity Relationship; D064878:Web Browser
chemical_list: D008565:Membrane Proteins; D020543:Proteome