FAQs

What is the TmAlphaFold database?

TmAlphaFold database is the collection of alpha-helical transmembrane proteins from the AlphaFold database. It contains structures predicted by AlphaFold2, together with information about the membrane plane - determined by TMDET algorithm - and an evaluation of structure data regarding the double lipid layer as structural constraint.

Why is my favorite membrane protein missing from the TmAlphaFold database?

Please look up whether your protein is included in the AlphaFold database at EBI. In case the protein can be found there, it was probably missed by the CCTOP algorithm, used for filtering transmembrane proteins. CCTOP has very high accuracy to discriminate TM and non-TM proteins (~99%), however in such large scale datasets a few proteins may be missing. Please also note, that in the TmAlphaFold database we only store alpha-helical transmembrane proteins.

How are structures categorized into different quality levels?

We evaluate structures based on the determined membrane plane, whether there are non-TM segments embedding in the membrane, or in contrast if there are TM regions that are placed outside the membrane bilayer. For more information visit the methodology page.

I have my own predicted AlphaFold structure - how can I evaluate this structure?

You can submit the structure predicted by AlphaFold in TMDET home page to get the orientation of the protein relative to the lipid bilayer. Please note that we included additional steps to more precisely detect the membrane on the AlphaFold predicted structures. Users can also use the CCTOP web server to predict the topology of the protein, using only the sequence of the protein. If you have your custom AlphaFold prediction and the above-mentioned servers do not give a satisfying result, send an email to us with the AlphaFold structure file (in PDB format) and PAE matrix (json format). Please note that you may have to wait for the result. Please also consider that the current version of TMAlphaFold can only handle monomer structures at the moment.

How can I download the database?

Membrane orientation, CCTOP prediction results, rotated structure in pdb format and the evaluation can be downloaded for each entry using the download () tab at the entry viewer page. We also prepared sets to bulk download structures separated by organisms, which can be downloaded from download page.

How can I cite TmAlphaFold database?

If you make use of TmAlphaFold database, please cite:

Dobson L, Szekeres LI, Gerdán C, Langó T, Zeke A and Tusnady GE (2022) TmAlphaFold database: membrane localization and evaluation of AlphaFold2 predicted alpha-helical transmembrane protein structures. Nucleic Acids Research, gkac928 [Journal][DOI].