MorphOT

MorphOT interpolates between EM density maps using an optimal transport-based metric to produce realistic morphing trajectories that reveal continuous conformational changes in molecular structures.

Key Features:

• Optimal transport-based interpolation: Uses an optimal transport metric to displace densities and interpolate between EM maps instead of linearly blending them.
• Improved morphing quality: Adapts and optimizes shape interpolation techniques for EM density maps to produce continuous trajectories that clarify conformational changes.
• ChimeraX integration: Implements MorphOT as a ChimeraX plugin to enable interpolation of multiple density maps within ChimeraX.
• CPU and GPU support: Implementation supports computation on both CPU and GPU resources.

Scientific Applications:

• Conformational heterogeneity analysis: Produces continuous morphing trajectories to analyze structural variability across EM maps.
• Investigation of molecular mechanisms: Reveals sequential conformational changes relevant to molecular mechanisms by interpolating density maps.
• Protein-ligand interaction studies: Visualizes conformational transitions associated with protein-ligand binding and other large structural changes.

Methodology:

Computes optimal transport-based interpolations between EM density maps, adapts shape-interpolation techniques for density data, and runs on CPU or GPU as implemented in a ChimeraX plugin.