What is HTP?

HTP stands for Human Transmembrane Proteome. It contains all the sequences of human α-helical transmembrane proteins together with their predicted and/or experimentally established topologies, and their predicted and/or experimental solved 3D structures. More information about the database can be found in the manual and in the manuscripts.

How can I cite HTP?

Dobson L, Langó T, Reményi I and Tusnády GE (2015)

The human transmembrane proteome
Biology Direct 10, 31.
[Journal] [PubMed] [PDF]

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]

What is evidence level?

Evidence level of an entry in HTP database can be the following:

3D structure

3D structure of the transmembrane protein was determined by X-ray diffraction, by electron diffraction or by NMR. In this case a CrossRef to the appropriate PDBTM entry(ies) is(are) given.

Experiment

There is(are) experimental result(s) about the topology. In this case a CrossRef to the appropriate PDB, TOPDB entries should be given.

TOPDOM

There are domains and sequence motifs located conservatively in one side of transmembrane proteins from TOPDOM.

Exists

There is evidence to the existence of the protein.

Prediction

There is no evidence to the existence of the protein. Both the amino acid sequence and the topology are predicted from the human genome sequence.

What is reliability of topology?

Reliability of topology prediction is calculated by summing up the posterior probabilities along the state path determined by the Viterbi algorithm in the HMMTOP program. It can be seen in the plot below, that the reliability highly correlate with the prediction accuracy, measured in a human benchmark set. For more information, please read the article describing the HTP database. Predictions are sorted by reliability and the topology prediction accuracies on the bechmark set (red line), the reliability on the same set (blue line) and the reliability measured on the whole transmembrane proteome (magenta line) are plotted for the subset, whose reliability are larger or equal than the current reliability value.

What file format is used in HTP database?

HTP use an xml file format specified by schema definition, which can be found here.

What is the difference between HTP and UniTmp?

The UNIfied database of TransMembrane Proteins (UniTmp) is a comprehensive and freely accessible resource of transmembrane protein topology and structural information. UniTmp bridges the gap between TOPDB (Topology Data Bank of Transmembrane Proteins), TOPDOM (database of conservatively located domains and motifs in proteins), PDBTM (Protein Data Bank of Transmembrane Proteins) and HTP (Human Transmembrane Proteome) databases. These resources stand for over 10 years by now and they provide structural information at different levels. The goal of UniTmp was to serve a solid background for all this information, by integrating these resources using a shared SQL based database. This way UniTmp provides up-to-date and consistent data, while keeping up the old usual interface of the original websites.