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Graph based Molecular Alignment (GMA)

GMA is a combined 2D/3D approach for the fast superposition of flexible chemical structures, which is based on recent progress in the efficient identification of common subgraphs and a gradient-based torsion space optimization algorithm. The simplicity of the approach is reflected in its generality and computational efficiency. The approach neither requires precalculated conformations of the molecules nor does it make simplifying assumptions on the topology of the molecules being compared. Graph-based molecular alignment produces alignments that are consistent with the chemistry of the molecules as well as their general structure, as it depends on both the local connectivities between atoms and the overall topology of the molecules. Results from extensive evaluation suggest that, for most practical purposes, graph-based molecular alignment is a viable alternative to molecular field alignment with respect to structural superposition and leads to structures of comparable quality in a fraction of the time, taking on average less than 0.1 sec per molecule pair. GMA can claim to be the fastest available explicitly flexible molecular alignment method.