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Molecular dynamics of two ester hydrolases: comparison using the BioSimGrid database Kaihsu Tai The systems H142 N156 S144 S203 H447 OMPLA E334 ● both serine esterases (ester hydrolases, EC 3.1.1) ● with the catalytic triad: Ser - His - Glu|Asn AChE The trajectories trajectory description Apo-AChE unliganded monomer Fas-AChE liganded with fasciculin 2 time/ns id code 15 GB-OXF_11 5 GB-OXF_12 OMPLA1 unliganded monomer, Ewald 10 GB-OXF_16 OMPLA2 unliganded dimer, Ewald 10 GB-OXF_17 OMPLA3 liganded dimer, Ewald 10 GB-OXF_15 OMPLA4 unliganded monomer, cutoff 5.7 GB-OXF_9 OMPLA5 unliganded dimer, cutoff 5 GB-OXF_10 OMPLA6 liganded dimer, cutoff 5 GB-OXF_14 ● ...not yet data deluge ● but... articles with “molecular dynamics” in title or abstract in the Biophysical Journal year 2004 (up to November) 2003 2002 2001 2000 1995 to 1999 1990 to 1994 1976 to 1989 number ~97 ~96 ~70 ~55 ~47 ~186 ~48 <25 (one of the first protein MD: 1980 McCammon et al.) Things we tried that did not work very well ● Picking candidate atoms from the side chain of the triad and generate – the meta-plot – the meta-histogram Meta-plot Meta-histogram A set of metrics for triad intactness A set of metrics for triad intactness Looking ahead ● ● Here we had some intuition, and formed a model. – Is it possible to do model-free data mining? – n × n rmsd (as Bing may have shown), etc. – Yes, we can do it, but what is the biological/biochemical relevance? The answer is 42 - what is the question?