Frequently Asked Questions

Currently, structures can be uploaded only in cif or cif.gz format.

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.

The maximum size of the input file is 20 MB.

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 (this switch is only active if the structure contains a single chain).

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.

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.

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.

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