OTMol formulates molecular superimposition as fused supervised Gromov-Wasserstein optimal transport, yielding atom-order-independent, chirality-preserving alignments with preserved bond connectivity across ligands, peptides, lipids, and water or noble gas clusters.
Algorithm for efficient superposition and clustering of molecular assem- blies using the branch-and-bound method
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OTMol: Robust Molecular Structure Comparison via Optimal Transport
OTMol formulates molecular superimposition as fused supervised Gromov-Wasserstein optimal transport, yielding atom-order-independent, chirality-preserving alignments with preserved bond connectivity across ligands, peptides, lipids, and water or noble gas clusters.