Determining Membrane Orientation of Transmembrane Proteins

Frequently Asked Questions

Which input types are supported on TmDet server?

Currently, structures can be uploaded in plane or gzipped CIF or ENT format.

NOTE:

CIF files must include _entity and _entity_poly tags. Files submitted without these tags will fail.

How many jobs can I run on TmDet server?

Due to limited server capacity, a maximum of 50 jobs can run simultaneously, and each user can submit a maximum of 100 jobs per day.

What is the maximum file size allowed?

The maximum size of the input file is 20 MB.

How should I define inputs for TmDet server?

After uploading the input file, a Mol* structure viewer will open along with a dropdown menu where user can select chains to exclude from the analysis (e.g., antibodies). There is a separate switch for detecting curved membranes or for finding membrane-embedded structures using fragmentation.

How can I run a job again with different parameters?

In the task list, clicking the rerun icon next to a completed task opens the input page containing the protein structure and parameters used, allowing users to modify parameters and rerun the analysis with different settings.

How do I interpret all the outputs in the downloaded zip file?

The downloadable ZIP file contains annotated region data in XML format and a modified CIF file including the transformed protein structure (the z-axis is aligned with the normal vector of the membrane plane, and the origin of the coordinate system is at the center of the membrane), as well as two rows of silver atoms representing the membrane.

What is the difference between TmDet Server and the Pdbtm/TmAlphaFold database?

The Pdbtm database contains structures from the PDB database annotated with a previous version of TmDet, while the TmAlphaFold database uses a different version of TmDet that utilized pLDDT and PAE values to annotate structures from the AlphaFold database. The TmDet server uses the latest version of the program, which only relies on atomic coordinates and can handle proteins embedded in double membranes and detect curved membranes.

Why is a signal peptide recognized as a transmembrane helix in AlphaFold predicted structures?

TmDet is not a signal peptide predictor. Please remove the signal peptide from the input structure file before submitting it.

How should I cite TmDet server?

If you find the TmDet server useful and use it in your work, please cite the following article:

Tusnady GE and Gerdan C (2025)
TmDet 4.0: Determining Membrane Orientation of Transmembrane Proteins from 3D structure.
Nucleic Acids Research, submitted.