Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures.

BMC Bioinformatics · 2004 · PMC344530 · PMID 14715091

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To the contrary, the corresponding RMSD values calculated for the alignment of all IgV's and globin domains against the IgV core (match states from the IgV 3D HMM) resulted in quite significant overlap and appeared to be much less informative for structural classification (Figure 5 ).

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