TmDet

TmDet determines the orientation of transmembrane proteins within lipid bilayers based on their 3D structure, providing information about structural elements and assessing model embeddability.

Key Features:

• Membrane Orientation Determination: Determines the relative position of membrane proteins with respect to the lipid bilayer using atomic coordinates.
• Structural Element Classification: Provides information about the type of structural elements in transmembrane proteins.
• Model Embeddability Assessment: Determines whether modeled structures can be embedded into the membrane.
• Support for Diverse Transmembrane Protein Types: Supports various transmembrane protein types including bacterial multidrug efflux pumps embedded in both outer and inner membranes and piezo-type mechanosensitive ion channels in highly curved membranes.
• AI-Predicted Structure Compatibility: Addresses challenges arising from AI-predicted protein structures including determination of model accuracy and membrane orientation of modeled structures containing errors.

Scientific Applications:

• Transmembrane Protein Structure Analysis: Determines how a transmembrane protein is oriented in the membrane for experimentally determined structures.
• AI-Predicted Model Validation: Determines the accuracy of model structures when the actual three-dimensional structure is unknown.
• Membrane Protein Modeling: Determines the membrane orientation of modeled transmembrane protein structures that contain errors.

Methodology:

TmDet uses the atomic coordinates of the protein to determine the relative position of membrane proteins with respect to the lipid bilayer.