MembraneFold

MembraneFold visualizes membrane protein three-dimensional structures and overlays topology predictions to enable interpretation of transmembrane orientation and sequence annotation.

Key Features:

• Integration of Structure and Topology Predictions: Combines structural inputs from uploaded PDB files, AlphaFold DB, or OmegaFold with topology predictions from DeepTMHMM.
• Structure Prediction Fallback: Uses OmegaFold as a fallback structural predictor when neither an uploaded PDB file nor an AlphaFold DB entry is available.
• Topology Prediction: Incorporates DeepTMHMM-generated topology labels to assign membrane regions and orientation along the sequence.
• Dual Output Presentation: Produces a visual three-dimensional structure with topology superimposed and a corresponding sequence annotation.
• Holistic Analysis: Integrates structure and topology predictions to address limitations of tools that predict only structure or only topology.

Scientific Applications:

• Membrane protein structure and topology analysis: Provides combined structural and topology data for interpreting transmembrane orientation and locating functional or structural motifs.
• Drug discovery: Supplies three-dimensional structural models with membrane-context topology to support structure-based ligand and target analysis.
• Molecular biology and biophysics: Aids molecular biology studies and biophysical analyses of membrane-associated processes by annotating sequences with topology and structural context.

Methodology:

MembraneFold integrates structural predictions from uploaded PDB files, AlphaFold DB, or OmegaFold with topology predictions from DeepTMHMM and combines them for visualization and sequence annotation.