Molecular dynamics simulations is a valuable tool to study protein unfolding in silico. Analyzing the relative spatial position of the residues during the simulation may indicate which residues are essential in determining the protein structure. We present a method, inspired by a popular data mining technique called Frequent Itemset Mining, that clusters sets of amino acid residues with a synchronized trajectory during the unfolding process. The proposed approach has several advantages over traditional hierarchical clustering. © 2009 Springer Berlin Heidelberg.
CITATION STYLE
Ferreira, P. G., Silva, C. G., Azevedo, P. J., & Brito, R. M. M. (2009). Spatial clustering of molecular dynamics trajectories in protein unfolding simulations. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5488 LNBI, pp. 156–166). https://doi.org/10.1007/978-3-642-02504-4_14
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