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

Alexandrov V, Gerstein M,
BMC Bioinformatics (2004) 5(3):2 PublishedPSI:Phase 2  
Northeast Structural Genomics Consortium

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We have created a rigorous 3D HMM representation for protein structures and implemented a complete set of routines for building 3D HMMs in C and Perl. ...
statistics & numerical data chemistry classification methods 
Computational Biology Models, Molecular NAD Protein Structure, Quaternary Flavin-Adenine Dinucleotide Immunoglobulins Sequence Alignment Flavodoxin Protein Folding Imaging, Three-Dimensional Algorithms Muramidase Markov Chains Thioredoxins 
17 (Last update: 04/21/2018 2:54:42pm)  
BMC Bioinformatics. 2004 Jan 9;5:2.