What extra functionalities PDBTM provides over PDB?

PDBTM is a collection of transmembrane protein structures deposited into PDB. In addition to the selection of membrane proteins, PDBTM also provides information about the position of the lipid bilayer.

How membrane regions are defined?

PDBTM does not identify membrane regions in a way classical topology prediction algorithms do. PDBTM is based on the TMDET method, that is able to detect the most probable membrane plane on 3D structures deposited into PDB. Membrane regions are defined after the position of the membrane is defined.

Dobson L, Gerdán C, Tusnády S, Langó T, Zeke A, Szekeres L, Kuffa K and Tusnády GE (2024)

UniTmp: Unified resources for transmembrane proteins.
Nucleic Acids Research 52, D572-8
[Journal] [PubMed] [PDF]

Tusnády GE, Dosztányi Zs and Simon I (2015)

Transmembrane proteins in the Protein Data Bank: identification and classification
Bioinformatics 20, 2964-2972.
[Journal] [PubMed] [PDF]

Kozma D, Simon I,and Tusnády GE (2012)

PDBTM: Protein Data Bank of transmembrane proteins after 8 years
Nucleic Acids Research 41 Database Issue, D524-D529.
[Journal] [PubMed] [PDF]