PairMap2: A Web Application for Intermediate‐Molecule Insertion in Relative Binding Free Energy Calculations

PairMap2 is a web application for testing intermediate‐molecule insertion in relative binding free energy calculations. Transformations between structurally distant ligands can have insufficient overlap in free‐energy space, leading to poor convergence and unreliable predictions. PairMap2 reimplements the PairMap intermediate‐insertion workflow as a browser‐based tool and supports two‐molecule path analysis and multiligand perturbation‐map construction. The interface visualizes perturbation networks, generated intermediates, and maximum common substructure‐based atom mappings. In nine benchmark cases from the original PairMap study, PairMap2 completed faster in eight cases; for an additional low‐similarity transformation (lead optimization mapper (LOMAP) similarity score 0.0111), it achieved an approximately 19.6‐fold speedup. PairMap2 enables computational chemists to assess intermediate insertion before free energy perturbation FEB calculations without setting up a local execution environment.