MMMx

MMMx supports protein ensemble modeling and analysis for designing experiments that characterize the distributed structure of proteins with disordered domains.

Key Features:

• AlphaFold2 integration: MMMx starts ensemble modeling from AlphaFold2 predictions or folded domain structures.
• Weak order analysis: Weak order can be analyzed with reference to a random coil model or to peptide chains that match the residue-specific Ramachandran angle distribution of the loop regions and are otherwise unrestrained.
• Chain compaction/expansion detection: The deviation of the mean square end-to-end distance of chain sections from their average over sections of the same sequence length reveals localized compaction or expansion of the chain.
• Shape visualization: The shape sampled by disordered chains is visualized by superposition in the principal axes frame of their inertia tensor.
• Ensemble comparison: Ensembles of different sizes and with weighted conformers can be compared based on a similarity parameter that abstracts from the ensemble width.

Scientific Applications:

• Disordered protein characterization: MMMx supports the design of experiments to characterize the distributed structure of proteins with disordered domains.
• Conformational ensemble analysis: MMMx provides analysis and visualization tools for conformational ensembles of proteins with multiple folded domains whose relative spatial arrangement is distributed.

Methodology:

MMMx performs weak order analysis with reference to a random coil model or to peptide chains matching residue-specific Ramachandran angle distributions of loop regions, detects localized chain compaction or expansion through deviation of mean square end-to-end distance from sequence-length averages, visualizes disordered chain shapes by superposition in the principal axes frame of the inertia tensor, and compares ensembles using a similarity parameter that abstracts from ensemble width.