TOPDOM: Conservatively Located Domains and Motifs in Proteins

What is TOPDOM?

The TOPDOM database is a collection of domains and sequence motifs located conservatively in one side of membranes either in transmembrane or globular proteins.

Why is the localization description is only two-state (inside/outside) and does not include more detailed information for all cellular compartments?

Enzyme activity depends on the environment, that can be defined by the orientation (inside/outside) and surrounding macromolecus. This information is already helpful and sufficient to predict topology or generate benchmark sets. By further narrowing these definitions the statistically meaningful data would be significantly less.

How can I cite TOPDOM?

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 , submitted.
[Journal] [PubMed] [PDF] [Server]

Varga J, Dobson L and Tusnády GE (2016)

TOPDOM: database of topologically consistently located protein domains and motifs.
Bioinformatics 32, 2725-2726.
[Journal] [Medline] [PDF] [Server]

Tusnády GE, Kalmár L, Hegyi H, Tompa P and Simon I (2008)

TOPDOM: database of domains and motifs with conservative location in transmembrane proteins.
Bioinformatics 24, 1469-1470.
[Journal] [Medline] [PDF]