TSTMP


NAR Molecular Biology Database Collection entry number 1937
Julia Varga1,2, László Dobson2, István Reményi2 and Gábor E. Tusnády2
1 Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Muegyetem rakpart 3., H1111, Hungary 2 "Momentum" Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary

Database Description

TSTMP is a database designed to help the target selection of human transmembrane proteins for structural genomics projects. The database contains human transmembrane proteins with two or more transmembrane segments considering the existence of an exact 3D structure, or the possibility of an existing model structure for the protein, or the necessity of a new structure for modeling the protein. The database was built by sorting out human proteins with known structure and searching for suitable model structures for the remaining proteins. Proteins without 3D structure or proper model structure were then searched for homologues among the human transmembrane proteins to select targets whose successful structure determination would lead to the best structural coverage of the human transmembrane proteome.

Acknowledgements

This work was supported by the Hungarian Scientific Research Fund [K104586, http://www.otka.hu] and grant ÚNKP-16-2_VBK-016 of the New National Excellence Programme funded by the Ministry of Human Resources. GET was supported by “Momentum” Program of the Hungarian Academy of Sciences. Funding for open access charge: Hungarian Academy of Sciences.

References

1. Varga J, Dobson L, Remenyi I and Tusnady GE (2017) TSTMP: Target Selection for structural genomics of human TransMembrane Proteins. Nucl Acids Res (Database issue)
2. Dobson L, Remenyi I and Tusnady GE (2015) The human transmembrane proteome. Biol Direct 10, 31.
3. Kozma,D., Simon,I. and Tusnady,G.E. (2013) PDBTM: Protein Data Bank of transmembrane proteins after 8 years. Nucleic Acids Res., 41, D524–D529.
4. Dobson,L., Reményi,I. and Tusnády,G.E. (2015) CCTOP: a Consensus Constrained TOPology prediction web server. Nucleic Acids Res., 43, W408–W412.
5. Kozma,D. and Tusnády,G.E. (2015) TMFoldRec: a statistical potential-based transmembrane protein fold recognition tool. BMC Bioinformatics, 16, 201.
6. Remmert,M., Biegert,A., Hauser,A. and Söding,J. (2011) HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nat. Methods, 9, 173–175.

Subcategory: Protein structure

Go to the abstract in the NAR 2017 Database Issue.
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